library(pROC)## Warning: package 'pROC' was built under R version 3.5.2## Type 'citation("pROC")' for a citation.##
## Attaching package: 'pROC'## The following objects are masked from 'package:stats':
##
## cov, smooth, varLoad sample daat
load('../../../1_1Stats/STAT435-VDVdata.RData')
tr = sample(nrow(vdv.clin), round(2/3*nrow(vdv.clin)))
trDat = vdv.clin[tr,]
tsDat = vdv.clin[-tr,]Use signature genes
gDat<-data.frame(t(vdv.genes[sample(nrow(vdv.genes), 100),]))
gDat$RFS.event = vdv.clin$RFS.event
tr.gDat = gDat[tr,]
ts.gDat = gDat[-tr,]Make the formula
f = as.formula(paste("RFS.event ~",paste(names(tr.gDat)[-ncol(tr.gDat)], collapse=' + ')))Fitting the model
stepFit = glm(RFS.event ~ 1, family='binomial', data=tr.gDat)
stepFit = step(stepFit, scope=f)## Start: AIC=265.64
## RFS.event ~ 1
##
## Df Deviance AIC
## + NEK2 1 244.27 248.27
## + ACADSB 1 249.65 253.65
## + PPIA 1 252.11 256.11
## + APRT 1 252.38 256.38
## + SLC19A1 1 252.42 256.42
## + SLC22A4 1 252.71 256.71
## + RPS6 1 253.10 257.10
## + ABCD3 1 253.97 257.96
## + LDHA 1 254.09 258.09
## + PECI 1 255.68 259.68
## + RFC5 1 257.06 261.06
## + EWSR1 1 257.07 261.07
## + DUT 1 257.54 261.54
## + ACTR3 1 258.50 262.50
## + CLK3 1 258.53 262.53
## + HDAC6 1 259.01 263.01
## + IRF3 1 259.27 263.27
## + CACNG2 1 259.37 263.37
## + AGL 1 259.69 263.69
## + CR1 1 259.88 263.88
## + SLC6A14 1 260.09 264.09
## + VPS35 1 260.24 264.24
## + HOXB5 1 260.26 264.26
## + RPS11 1 260.41 264.41
## + RPS20 1 260.50 264.50
## + FPR1 1 260.97 264.97
## + MPP3 1 261.15 265.15
## + CACNA1C 1 261.36 265.36
## + SHC3 1 261.57 265.57
## + CDC42BPB 1 261.63 265.63
## <none> 263.64 265.64
## + KLRB1 1 261.77 265.77
## + PROX1 1 261.78 265.78
## + FH 1 261.83 265.83
## + CKB 1 261.85 265.85
## + DRD4 1 261.96 265.96
## + FCER1G 1 261.97 265.97
## + ZNF202 1 262.00 266.00
## + CHST2 1 262.17 266.17
## + SLC26A4 1 262.25 266.25
## + DLG2 1 262.35 266.35
## + ADD2 1 262.40 266.40
## + B4GALT2 1 262.40 266.40
## + CLDN14 1 262.49 266.49
## + BID 1 262.52 266.52
## + CYP39A1 1 262.58 266.58
## + MMD 1 262.60 266.60
## + AXIN1 1 262.63 266.63
## + HSD3B1 1 262.66 266.66
## + GATA4 1 262.67 266.67
## + ACYP1 1 262.70 266.70
## + TGM3 1 262.77 266.77
## + ATP12A 1 262.80 266.80
## + FBXW2 1 262.82 266.82
## + PBX1 1 262.85 266.85
## + TLR1 1 262.87 266.87
## + GOT2 1 262.87 266.87
## + SLC6A5 1 262.91 266.91
## + CDS1 1 262.93 266.93
## + JAK3 1 262.96 266.96
## + FGF6 1 263.00 267.00
## + KIR2DS3 1 263.06 267.06
## + MGAM 1 263.07 267.07
## + TMEM2 1 263.11 267.11
## + IFNA5 1 263.12 267.12
## + UCP1 1 263.14 267.14
## + DOM3Z 1 263.14 267.14
## + HOXC10 1 263.16 267.16
## + RAB7L1 1 263.18 267.18
## + PDE7A 1 263.23 267.23
## + GGA1 1 263.23 267.23
## + NAP1L4 1 263.23 267.23
## + ADCY8 1 263.27 267.27
## + TMOD2 1 263.30 267.30
## + CRK 1 263.33 267.33
## + CA11 1 263.36 267.36
## + CRYBA1 1 263.39 267.39
## + ADD1 1 263.40 267.40
## + TIA1 1 263.44 267.44
## + HNRPDL 1 263.48 267.48
## + LARGE 1 263.50 267.50
## + NUP98 1 263.53 267.53
## + TGFBR2 1 263.54 267.54
## + SPAG6 1 263.54 267.54
## + STAT3 1 263.57 267.57
## + ESR2 1 263.57 267.57
## + NOL4 1 263.58 267.58
## + CLIC2 1 263.58 267.58
## + PMAIP1 1 263.59 267.59
## + ACADL 1 263.59 267.59
## + BNIP2 1 263.60 267.60
## + SRI 1 263.60 267.60
## + SRD5A2 1 263.61 267.61
## + TFDP2 1 263.61 267.61
## + MAP7 1 263.62 267.62
## + GJA5 1 263.62 267.62
## + CAMK2B 1 263.63 267.63
## + MME 1 263.64 267.64
## + TNFRSF9 1 263.64 267.64
## + OAZ3 1 263.64 267.64
## + CD209 1 263.64 267.64
##
## Step: AIC=248.27
## RFS.event ~ NEK2
##
## Df Deviance AIC
## + ABCD3 1 235.46 241.46
## + DRD4 1 235.72 241.72
## + SLC22A4 1 235.85 241.85
## + ACADSB 1 236.46 242.46
## + CLK3 1 237.43 243.43
## + MPP3 1 238.09 244.09
## + RPS6 1 238.22 244.22
## + PPIA 1 238.55 244.55
## + SLC19A1 1 238.71 244.71
## + APRT 1 239.53 245.53
## + HDAC6 1 239.58 245.58
## + ZNF202 1 239.90 245.90
## + CKB 1 240.24 246.24
## + CACNG2 1 240.63 246.63
## + CR1 1 240.69 246.69
## + IRF3 1 240.90 246.90
## + LDHA 1 240.97 246.97
## + ADD1 1 241.21 247.21
## + CLDN14 1 241.27 247.27
## + CACNA1C 1 241.27 247.27
## + TMEM2 1 241.53 247.53
## + GATA4 1 241.75 247.75
## + SLC6A5 1 241.77 247.77
## + AGL 1 241.86 247.86
## + DLG2 1 241.94 247.94
## + PDE7A 1 242.00 248.00
## + ADD2 1 242.15 248.15
## + TGM3 1 242.16 248.16
## + PECI 1 242.17 248.17
## <none> 244.27 248.27
## + RPS20 1 242.33 248.33
## + FPR1 1 242.44 248.44
## + HSD3B1 1 242.47 248.47
## + ACYP1 1 242.62 248.62
## + CYP39A1 1 242.79 248.79
## + HOXB5 1 242.82 248.82
## + GGA1 1 242.85 248.85
## + HOXC10 1 242.92 248.92
## + SHC3 1 242.94 248.94
## + PMAIP1 1 242.95 248.95
## + SLC6A14 1 243.00 249.00
## + DUT 1 243.00 249.00
## + BNIP2 1 243.00 249.00
## + VPS35 1 243.11 249.11
## + HNRPDL 1 243.12 249.12
## + CDS1 1 243.13 249.13
## + ADCY8 1 243.18 249.18
## + CRYBA1 1 243.18 249.18
## + EWSR1 1 243.22 249.22
## + RFC5 1 243.37 249.37
## + TMOD2 1 243.38 249.38
## + NOL4 1 243.45 249.45
## + IFNA5 1 243.53 249.53
## + KLRB1 1 243.56 249.56
## + TIA1 1 243.59 249.59
## + PROX1 1 243.60 249.60
## + PBX1 1 243.64 249.64
## + B4GALT2 1 243.64 249.64
## + FH 1 243.65 249.65
## + RPS11 1 243.65 249.65
## + CDC42BPB 1 243.67 249.67
## + JAK3 1 243.73 249.73
## + TFDP2 1 243.77 249.77
## + ACTR3 1 243.78 249.78
## + MMD 1 243.78 249.78
## + GJA5 1 243.81 249.81
## + LARGE 1 243.83 249.83
## + FCER1G 1 243.86 249.86
## + NUP98 1 243.88 249.88
## + ATP12A 1 243.88 249.88
## + SRI 1 243.93 249.93
## + SLC26A4 1 243.96 249.96
## + STAT3 1 243.99 249.99
## + CRK 1 244.01 250.01
## + FBXW2 1 244.03 250.03
## + NAP1L4 1 244.04 250.04
## + MME 1 244.06 250.06
## + CA11 1 244.07 250.07
## + CLIC2 1 244.08 250.08
## + CHST2 1 244.12 250.12
## + MGAM 1 244.12 250.12
## + BID 1 244.14 250.14
## + MAP7 1 244.15 250.15
## + AXIN1 1 244.15 250.15
## + ACADL 1 244.16 250.16
## + ESR2 1 244.17 250.17
## + RAB7L1 1 244.18 250.18
## + GOT2 1 244.18 250.18
## + CAMK2B 1 244.19 250.19
## + DOM3Z 1 244.21 250.21
## + KIR2DS3 1 244.24 250.24
## + TLR1 1 244.25 250.25
## + CD209 1 244.25 250.25
## + UCP1 1 244.25 250.25
## + SRD5A2 1 244.25 250.25
## + FGF6 1 244.25 250.25
## + SPAG6 1 244.26 250.26
## + OAZ3 1 244.26 250.26
## + TNFRSF9 1 244.26 250.26
## + TGFBR2 1 244.27 250.27
## - NEK2 1 263.64 265.64
##
## Step: AIC=241.46
## RFS.event ~ NEK2 + ABCD3
##
## Df Deviance AIC
## + MPP3 1 228.22 236.22
## + HDAC6 1 228.76 236.76
## + SLC22A4 1 228.93 236.93
## + RPS6 1 229.61 237.61
## + DRD4 1 229.88 237.88
## + CLK3 1 229.96 237.96
## + ADD1 1 230.72 238.72
## + DUT 1 230.87 238.87
## + CKB 1 231.53 239.53
## + PPIA 1 231.62 239.62
## + CACNG2 1 231.72 239.72
## + CACNA1C 1 231.96 239.96
## + SLC19A1 1 232.08 240.08
## + LDHA 1 232.26 240.26
## + RPS20 1 232.26 240.26
## + HOXB5 1 232.27 240.27
## + TMEM2 1 232.37 240.37
## + ZNF202 1 232.60 240.60
## + IRF3 1 232.62 240.62
## + DLG2 1 232.65 240.65
## + ACADSB 1 232.85 240.85
## + CR1 1 233.02 241.02
## + APRT 1 233.05 241.05
## + HSD3B1 1 233.19 241.19
## <none> 235.46 241.46
## + CYP39A1 1 233.66 241.66
## + CRYBA1 1 233.88 241.88
## + GJA5 1 233.89 241.89
## + SLC6A5 1 233.94 241.94
## + VPS35 1 234.00 242.00
## + NAP1L4 1 234.03 242.03
## + EWSR1 1 234.13 242.13
## + FH 1 234.13 242.13
## + KLRB1 1 234.18 242.18
## + PDE7A 1 234.24 242.24
## + MMD 1 234.25 242.25
## + RFC5 1 234.35 242.35
## + ATP12A 1 234.36 242.36
## + NOL4 1 234.42 242.42
## + B4GALT2 1 234.50 242.50
## + TNFRSF9 1 234.54 242.54
## + TLR1 1 234.55 242.55
## + GOT2 1 234.59 242.59
## + CDC42BPB 1 234.62 242.62
## + PMAIP1 1 234.70 242.70
## + PROX1 1 234.75 242.75
## + SHC3 1 234.78 242.78
## + TIA1 1 234.80 242.80
## + HNRPDL 1 234.91 242.91
## + TMOD2 1 234.91 242.91
## + ADD2 1 234.95 242.95
## + ACYP1 1 234.95 242.95
## + PECI 1 234.98 242.98
## + FBXW2 1 234.98 242.98
## + GATA4 1 235.00 243.00
## + SLC6A14 1 235.02 243.02
## + CLDN14 1 235.03 243.03
## + RPS11 1 235.06 243.06
## + LARGE 1 235.12 243.12
## + ESR2 1 235.13 243.13
## + MGAM 1 235.16 243.16
## + HOXC10 1 235.18 243.18
## + BNIP2 1 235.19 243.19
## + SLC26A4 1 235.22 243.22
## + AXIN1 1 235.24 243.24
## + GGA1 1 235.25 243.25
## + FGF6 1 235.25 243.25
## + NUP98 1 235.26 243.26
## + RAB7L1 1 235.26 243.26
## + ADCY8 1 235.26 243.26
## + MME 1 235.27 243.27
## + MAP7 1 235.27 243.27
## + KIR2DS3 1 235.32 243.32
## + CD209 1 235.33 243.33
## + TGM3 1 235.33 243.33
## + OAZ3 1 235.36 243.36
## + PBX1 1 235.37 243.37
## + CHST2 1 235.37 243.37
## + FCER1G 1 235.39 243.39
## + CAMK2B 1 235.39 243.39
## + CRK 1 235.40 243.40
## + SRD5A2 1 235.41 243.41
## + AGL 1 235.41 243.41
## + UCP1 1 235.42 243.42
## + CA11 1 235.42 243.42
## + TFDP2 1 235.43 243.43
## + CLIC2 1 235.43 243.43
## + ACTR3 1 235.44 243.44
## + TGFBR2 1 235.44 243.44
## + JAK3 1 235.44 243.44
## + DOM3Z 1 235.44 243.44
## + FPR1 1 235.45 243.45
## + SRI 1 235.45 243.45
## + BID 1 235.46 243.46
## + IFNA5 1 235.46 243.46
## + CDS1 1 235.46 243.46
## + SPAG6 1 235.46 243.46
## + ACADL 1 235.46 243.46
## + STAT3 1 235.46 243.46
## - ABCD3 1 244.27 248.27
## - NEK2 1 253.97 257.96
##
## Step: AIC=236.22
## RFS.event ~ NEK2 + ABCD3 + MPP3
##
## Df Deviance AIC
## + CACNG2 1 221.50 231.50
## + SLC22A4 1 221.56 231.56
## + DRD4 1 221.79 231.79
## + ADD1 1 222.39 232.39
## + HOXB5 1 222.46 232.46
## + HDAC6 1 222.56 232.56
## + RPS6 1 223.00 233.00
## + PROX1 1 223.28 233.28
## + LDHA 1 223.66 233.66
## + IRF3 1 224.09 234.09
## + ZNF202 1 224.12 234.12
## + CLK3 1 224.15 234.15
## + ACADSB 1 224.21 234.21
## + TMEM2 1 224.48 234.48
## + CACNA1C 1 224.50 234.50
## + CKB 1 224.95 234.95
## + RPS20 1 225.11 235.11
## + DUT 1 225.31 235.31
## + CR1 1 225.49 235.49
## + APRT 1 225.73 235.73
## + GJA5 1 225.75 235.75
## + VPS35 1 225.85 235.85
## + PPIA 1 225.96 235.96
## + DLG2 1 226.12 236.12
## <none> 228.22 236.22
## + SLC19A1 1 226.51 236.51
## + EWSR1 1 226.52 236.52
## + CDC42BPB 1 226.67 236.67
## + MMD 1 226.84 236.84
## + ACYP1 1 226.93 236.93
## + NAP1L4 1 226.96 236.96
## + TNFRSF9 1 227.06 237.06
## + NOL4 1 227.06 237.06
## + UCP1 1 227.07 237.07
## + FH 1 227.11 237.11
## + RFC5 1 227.19 237.19
## + SPAG6 1 227.21 237.21
## + SHC3 1 227.24 237.24
## + B4GALT2 1 227.25 237.25
## + KIR2DS3 1 227.33 237.33
## + FBXW2 1 227.35 237.35
## + HNRPDL 1 227.37 237.37
## + GOT2 1 227.40 237.40
## + ATP12A 1 227.40 237.40
## + CYP39A1 1 227.42 237.42
## + PMAIP1 1 227.42 237.42
## + PDE7A 1 227.50 237.50
## + CD209 1 227.52 237.52
## + KLRB1 1 227.57 237.57
## + RPS11 1 227.57 237.57
## + SLC6A14 1 227.60 237.60
## + OAZ3 1 227.71 237.71
## + PECI 1 227.72 237.72
## + HSD3B1 1 227.73 237.73
## + CA11 1 227.76 237.76
## + MME 1 227.80 237.80
## + TGFBR2 1 227.82 237.82
## + CLDN14 1 227.83 237.83
## + ADD2 1 227.89 237.89
## + TIA1 1 227.93 237.93
## + HOXC10 1 227.94 237.94
## + SLC26A4 1 227.99 237.99
## + SRD5A2 1 228.03 238.03
## + LARGE 1 228.03 238.03
## + FGF6 1 228.05 238.05
## + ACTR3 1 228.06 238.06
## + CAMK2B 1 228.08 238.08
## + CHST2 1 228.09 238.09
## + ACADL 1 228.10 238.10
## + TLR1 1 228.10 238.10
## + JAK3 1 228.11 238.11
## + ESR2 1 228.11 238.11
## + SRI 1 228.11 238.11
## + GATA4 1 228.12 238.12
## + BID 1 228.13 238.13
## + TMOD2 1 228.13 238.13
## + DOM3Z 1 228.13 238.13
## + CRYBA1 1 228.14 238.14
## + CDS1 1 228.14 238.14
## + CRK 1 228.14 238.14
## + FPR1 1 228.16 238.16
## + AXIN1 1 228.18 238.18
## + GGA1 1 228.18 238.18
## + AGL 1 228.18 238.18
## + MAP7 1 228.18 238.18
## + TFDP2 1 228.19 238.19
## + IFNA5 1 228.19 238.19
## + RAB7L1 1 228.19 238.19
## + SLC6A5 1 228.20 238.20
## + ADCY8 1 228.21 238.21
## + BNIP2 1 228.21 238.21
## + STAT3 1 228.21 238.21
## + FCER1G 1 228.21 238.21
## + CLIC2 1 228.21 238.21
## + TGM3 1 228.22 238.22
## + NUP98 1 228.22 238.22
## + MGAM 1 228.22 238.22
## + PBX1 1 228.22 238.22
## - MPP3 1 235.46 241.46
## - ABCD3 1 238.09 244.09
## - NEK2 1 250.99 256.99
##
## Step: AIC=231.5
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2
##
## Df Deviance AIC
## + DRD4 1 215.17 227.17
## + CKB 1 215.84 227.84
## + SLC22A4 1 215.99 227.99
## + GJA5 1 216.16 228.16
## + ADD1 1 216.41 228.41
## + HOXB5 1 216.77 228.77
## + RPS6 1 216.96 228.96
## + CLK3 1 217.09 229.09
## + PROX1 1 217.35 229.35
## + HDAC6 1 217.51 229.51
## + LDHA 1 217.64 229.64
## + DUT 1 217.79 229.79
## + ZNF202 1 217.86 229.86
## + ACADSB 1 217.98 229.98
## + DLG2 1 218.23 230.23
## + TMEM2 1 218.88 230.88
## + NOL4 1 218.90 230.90
## + RPS20 1 219.33 231.33
## + CACNA1C 1 219.41 231.41
## + SLC19A1 1 219.44 231.44
## + ACYP1 1 219.45 231.45
## <none> 221.50 231.50
## + IRF3 1 219.69 231.69
## + B4GALT2 1 219.75 231.75
## + PPIA 1 219.88 231.88
## + HNRPDL 1 219.97 231.97
## + GATA4 1 220.20 232.20
## + KIR2DS3 1 220.22 232.22
## + FH 1 220.23 232.23
## + KLRB1 1 220.25 232.25
## + CR1 1 220.29 232.29
## + VPS35 1 220.30 232.30
## + APRT 1 220.30 232.30
## + RAB7L1 1 220.33 232.33
## + NAP1L4 1 220.44 232.44
## + MMD 1 220.55 232.55
## + CRYBA1 1 220.64 232.64
## + TNFRSF9 1 220.64 232.64
## + RPS11 1 220.65 232.65
## + CAMK2B 1 220.66 232.66
## + CYP39A1 1 220.69 232.69
## + TGFBR2 1 220.69 232.69
## + EWSR1 1 220.70 232.70
## + UCP1 1 220.71 232.71
## + ATP12A 1 220.71 232.71
## + SHC3 1 220.72 232.72
## + ADD2 1 220.77 232.77
## + MME 1 220.80 232.80
## + DOM3Z 1 220.89 232.89
## + PECI 1 220.90 232.90
## + TIA1 1 220.93 232.93
## + SLC6A14 1 220.94 232.94
## + NUP98 1 220.95 232.95
## + CLDN14 1 220.96 232.96
## + SPAG6 1 220.99 232.99
## + CDS1 1 221.00 233.00
## + GOT2 1 221.06 233.06
## + SLC6A5 1 221.08 233.08
## + CDC42BPB 1 221.09 233.09
## + PMAIP1 1 221.11 233.11
## + OAZ3 1 221.16 233.16
## + CD209 1 221.17 233.17
## + ADCY8 1 221.17 233.17
## + FBXW2 1 221.19 233.19
## + HSD3B1 1 221.20 233.20
## + LARGE 1 221.24 233.24
## + FPR1 1 221.26 233.26
## + HOXC10 1 221.27 233.27
## + CA11 1 221.35 233.35
## + STAT3 1 221.35 233.35
## + SLC26A4 1 221.36 233.36
## + AGL 1 221.39 233.39
## + BID 1 221.40 233.40
## + RFC5 1 221.41 233.41
## + JAK3 1 221.41 233.41
## + SRD5A2 1 221.41 233.41
## + PBX1 1 221.41 233.41
## + ESR2 1 221.43 233.43
## + TLR1 1 221.43 233.43
## + MGAM 1 221.43 233.43
## + GGA1 1 221.43 233.43
## + CHST2 1 221.44 233.44
## + ACADL 1 221.45 233.45
## + MAP7 1 221.46 233.46
## + TGM3 1 221.48 233.48
## + FCER1G 1 221.48 233.48
## + CLIC2 1 221.48 233.48
## + FGF6 1 221.49 233.49
## + BNIP2 1 221.49 233.49
## + TMOD2 1 221.49 233.49
## + ACTR3 1 221.50 233.50
## + AXIN1 1 221.50 233.50
## + CRK 1 221.50 233.50
## + PDE7A 1 221.50 233.50
## + TFDP2 1 221.50 233.50
## + IFNA5 1 221.50 233.50
## + SRI 1 221.50 233.50
## - CACNG2 1 228.22 236.22
## - MPP3 1 231.72 239.72
## - ABCD3 1 232.14 240.14
## - NEK2 1 244.01 252.01
##
## Step: AIC=227.17
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4
##
## Df Deviance AIC
## + GJA5 1 207.68 221.68
## + DUT 1 209.50 223.50
## + CKB 1 209.64 223.64
## + HOXB5 1 210.01 224.01
## + HDAC6 1 210.57 224.57
## + ADD1 1 210.89 224.89
## + RPS6 1 210.91 224.91
## + CLK3 1 211.11 225.11
## + PROX1 1 211.41 225.41
## + SLC22A4 1 211.69 225.69
## + RPS20 1 211.88 225.88
## + LDHA 1 212.09 226.09
## + TNFRSF9 1 212.74 226.74
## + NOL4 1 212.79 226.79
## + TMEM2 1 213.07 227.07
## + DLG2 1 213.12 227.12
## + EWSR1 1 213.14 227.14
## <none> 215.17 227.17
## + CACNA1C 1 213.24 227.24
## + ACADSB 1 213.25 227.25
## + IRF3 1 213.29 227.29
## + PPIA 1 213.52 227.52
## + ACYP1 1 213.69 227.69
## + SLC19A1 1 213.90 227.90
## + APRT 1 213.97 227.97
## + RPS11 1 213.97 227.97
## + MAP7 1 214.00 228.00
## + RFC5 1 214.00 228.00
## + VPS35 1 214.02 228.02
## + NAP1L4 1 214.08 228.08
## + CRYBA1 1 214.09 228.09
## + CAMK2B 1 214.10 228.10
## + KIR2DS3 1 214.11 228.11
## + FH 1 214.15 228.15
## + KLRB1 1 214.27 228.27
## + GOT2 1 214.29 228.29
## + CYP39A1 1 214.34 228.34
## + CDC42BPB 1 214.34 228.34
## + GATA4 1 214.37 228.37
## + ZNF202 1 214.44 228.44
## + SHC3 1 214.46 228.46
## + RAB7L1 1 214.47 228.47
## + B4GALT2 1 214.49 228.49
## + CD209 1 214.51 228.51
## + CR1 1 214.51 228.51
## + ATP12A 1 214.53 228.53
## + MMD 1 214.53 228.53
## + SPAG6 1 214.54 228.54
## + UCP1 1 214.60 228.60
## + OAZ3 1 214.63 228.63
## + PECI 1 214.65 228.65
## + CHST2 1 214.67 228.67
## + TGFBR2 1 214.69 228.69
## + SLC6A14 1 214.72 228.72
## + HNRPDL 1 214.78 228.78
## + PBX1 1 214.84 228.84
## + ADD2 1 214.87 228.87
## + MME 1 214.91 228.91
## + FBXW2 1 214.93 228.93
## + SLC6A5 1 214.97 228.97
## + DOM3Z 1 214.97 228.97
## + MGAM 1 214.98 228.98
## + IFNA5 1 214.99 228.99
## + ESR2 1 215.00 229.00
## + LARGE 1 215.00 229.00
## + ACTR3 1 215.00 229.00
## + AGL 1 215.02 229.02
## + STAT3 1 215.02 229.02
## + CDS1 1 215.04 229.04
## + BNIP2 1 215.06 229.06
## + HSD3B1 1 215.07 229.07
## + NUP98 1 215.08 229.08
## + PDE7A 1 215.08 229.08
## + JAK3 1 215.11 229.11
## + TGM3 1 215.13 229.13
## + ADCY8 1 215.13 229.13
## + ACADL 1 215.13 229.13
## + PMAIP1 1 215.13 229.13
## + TIA1 1 215.13 229.13
## + AXIN1 1 215.14 229.14
## + GGA1 1 215.14 229.14
## + FPR1 1 215.14 229.14
## + TLR1 1 215.14 229.14
## + HOXC10 1 215.15 229.15
## + SLC26A4 1 215.15 229.15
## + FGF6 1 215.16 229.16
## + SRI 1 215.16 229.16
## + BID 1 215.16 229.16
## + CLIC2 1 215.16 229.16
## + CRK 1 215.16 229.16
## + CLDN14 1 215.16 229.16
## + TMOD2 1 215.17 229.17
## + SRD5A2 1 215.17 229.17
## + CA11 1 215.17 229.17
## + TFDP2 1 215.17 229.17
## + FCER1G 1 215.17 229.17
## - DRD4 1 221.50 231.50
## - CACNG2 1 221.79 231.79
## - ABCD3 1 222.38 232.38
## - MPP3 1 226.33 236.33
## - NEK2 1 243.58 253.58
##
## Step: AIC=221.68
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5
##
## Df Deviance AIC
## + PPIA 1 200.05 216.05
## + CKB 1 201.34 217.34
## + HOXB5 1 201.56 217.56
## + SLC22A4 1 202.28 218.28
## + CLK3 1 203.81 219.81
## + DLG2 1 204.14 220.14
## + DUT 1 204.38 220.38
## + NAP1L4 1 204.58 220.58
## + RPS6 1 204.61 220.61
## + ACADSB 1 205.06 221.06
## + NOL4 1 205.14 221.14
## + CRYBA1 1 205.41 221.41
## + GATA4 1 205.45 221.45
## + PROX1 1 205.50 221.50
## <none> 207.68 221.68
## + LDHA 1 205.82 221.82
## + APRT 1 205.94 221.94
## + IRF3 1 205.95 221.95
## + RAB7L1 1 206.11 222.11
## + HDAC6 1 206.16 222.16
## + KLRB1 1 206.17 222.17
## + FH 1 206.21 222.21
## + CACNA1C 1 206.24 222.24
## + UCP1 1 206.26 222.26
## + CYP39A1 1 206.32 222.32
## + CLDN14 1 206.33 222.33
## + SLC19A1 1 206.43 222.43
## + VPS35 1 206.58 222.58
## + RPS20 1 206.59 222.59
## + CD209 1 206.60 222.60
## + TLR1 1 206.62 222.62
## + OAZ3 1 206.65 222.65
## + CR1 1 206.69 222.69
## + KIR2DS3 1 206.70 222.70
## + ADD2 1 206.75 222.75
## + SHC3 1 206.79 222.79
## + ADD1 1 206.80 222.80
## + PDE7A 1 206.86 222.86
## + TNFRSF9 1 206.87 222.87
## + ESR2 1 206.94 222.94
## + ACYP1 1 206.96 222.96
## + SPAG6 1 206.97 222.97
## + TMEM2 1 207.00 223.00
## + B4GALT2 1 207.02 223.02
## + HOXC10 1 207.06 223.06
## + CDC42BPB 1 207.08 223.08
## + RFC5 1 207.11 223.11
## + TGM3 1 207.26 223.26
## + ADCY8 1 207.28 223.28
## + RPS11 1 207.28 223.28
## + MME 1 207.29 223.29
## + FGF6 1 207.31 223.31
## + MGAM 1 207.32 223.32
## + SLC6A5 1 207.34 223.34
## + TFDP2 1 207.37 223.37
## + GOT2 1 207.37 223.37
## + BNIP2 1 207.40 223.40
## + ZNF202 1 207.41 223.41
## + HSD3B1 1 207.45 223.45
## + LARGE 1 207.45 223.45
## + CHST2 1 207.45 223.45
## + JAK3 1 207.47 223.47
## + SLC6A14 1 207.50 223.50
## + FPR1 1 207.50 223.50
## + MMD 1 207.51 223.51
## + BID 1 207.53 223.53
## + SRI 1 207.53 223.53
## + GGA1 1 207.54 223.54
## + FCER1G 1 207.54 223.54
## + CRK 1 207.54 223.54
## + PECI 1 207.54 223.54
## + EWSR1 1 207.54 223.54
## + NUP98 1 207.57 223.57
## + STAT3 1 207.57 223.57
## + HNRPDL 1 207.58 223.58
## + TIA1 1 207.59 223.59
## + CAMK2B 1 207.60 223.60
## + PBX1 1 207.60 223.60
## + PMAIP1 1 207.61 223.61
## + CDS1 1 207.61 223.61
## + TGFBR2 1 207.62 223.62
## + IFNA5 1 207.62 223.62
## + ACTR3 1 207.64 223.64
## + DOM3Z 1 207.64 223.64
## + ACADL 1 207.65 223.65
## + MAP7 1 207.66 223.66
## + FBXW2 1 207.66 223.66
## + AGL 1 207.66 223.66
## + CLIC2 1 207.66 223.66
## + SRD5A2 1 207.67 223.67
## + CA11 1 207.67 223.67
## + ATP12A 1 207.67 223.67
## + SLC26A4 1 207.67 223.67
## + AXIN1 1 207.68 223.68
## + TMOD2 1 207.68 223.68
## - GJA5 1 215.17 227.17
## - DRD4 1 216.16 228.16
## - ABCD3 1 217.81 229.81
## - CACNG2 1 217.88 229.88
## - MPP3 1 222.17 234.17
## - NEK2 1 241.01 253.01
##
## Step: AIC=216.05
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA
##
## Df Deviance AIC
## + CKB 1 194.12 212.12
## + HOXB5 1 194.41 212.41
## + DLG2 1 195.19 213.19
## + SLC22A4 1 195.46 213.46
## + NOL4 1 196.10 214.10
## + GATA4 1 196.87 214.87
## + RPS20 1 197.30 215.30
## + TLR1 1 197.46 215.46
## + PROX1 1 197.48 215.48
## + FH 1 197.50 215.50
## + DUT 1 197.64 215.64
## + RPS6 1 197.66 215.66
## + RAB7L1 1 197.73 215.73
## + CRYBA1 1 197.83 215.83
## + CLDN14 1 197.84 215.84
## + NAP1L4 1 197.87 215.87
## + CACNA1C 1 197.94 215.94
## <none> 200.05 216.05
## + IRF3 1 198.28 216.28
## + ACADSB 1 198.48 216.48
## + CLK3 1 198.59 216.59
## + SPAG6 1 198.63 216.63
## + BID 1 198.68 216.68
## + ESR2 1 198.75 216.75
## + KLRB1 1 198.75 216.75
## + ADD2 1 198.77 216.77
## + ADD1 1 199.00 217.00
## + RPS11 1 199.00 217.00
## + CDC42BPB 1 199.03 217.03
## + CYP39A1 1 199.10 217.10
## + CHST2 1 199.11 217.11
## + HDAC6 1 199.14 217.14
## + HOXC10 1 199.17 217.17
## + SLC6A5 1 199.20 217.20
## + CR1 1 199.21 217.21
## + OAZ3 1 199.22 217.22
## + SHC3 1 199.27 217.27
## + ADCY8 1 199.29 217.29
## + BNIP2 1 199.31 217.31
## + UCP1 1 199.34 217.34
## + GGA1 1 199.36 217.36
## + FGF6 1 199.40 217.40
## + KIR2DS3 1 199.40 217.40
## + ACADL 1 199.43 217.43
## + ACTR3 1 199.45 217.45
## + PMAIP1 1 199.45 217.45
## + SRI 1 199.46 217.46
## + CD209 1 199.51 217.51
## + MME 1 199.56 217.56
## + TMEM2 1 199.61 217.61
## + LDHA 1 199.62 217.62
## + STAT3 1 199.66 217.66
## + TGM3 1 199.67 217.67
## + EWSR1 1 199.67 217.67
## + JAK3 1 199.68 217.68
## + FPR1 1 199.71 217.71
## + TFDP2 1 199.75 217.75
## + NUP98 1 199.79 217.79
## + DOM3Z 1 199.81 217.81
## + APRT 1 199.82 217.82
## + ZNF202 1 199.82 217.82
## + MGAM 1 199.83 217.83
## + FCER1G 1 199.84 217.84
## + VPS35 1 199.84 217.84
## + HNRPDL 1 199.85 217.85
## + IFNA5 1 199.86 217.86
## + PECI 1 199.87 217.87
## + SLC19A1 1 199.88 217.88
## + CAMK2B 1 199.88 217.88
## + FBXW2 1 199.90 217.90
## + ACYP1 1 199.90 217.90
## + MMD 1 199.92 217.92
## + PDE7A 1 199.93 217.93
## + GOT2 1 199.93 217.93
## + TMOD2 1 199.96 217.96
## + RFC5 1 199.96 217.96
## + TNFRSF9 1 199.97 217.97
## + TGFBR2 1 199.99 217.99
## + CLIC2 1 199.99 217.99
## + CRK 1 199.99 217.99
## + HSD3B1 1 200.00 218.00
## + B4GALT2 1 200.00 218.00
## + CDS1 1 200.01 218.01
## + AXIN1 1 200.02 218.02
## + PBX1 1 200.03 218.03
## + CA11 1 200.03 218.03
## + AGL 1 200.03 218.03
## + SLC6A14 1 200.03 218.03
## + LARGE 1 200.04 218.04
## + SRD5A2 1 200.04 218.04
## + MAP7 1 200.05 218.05
## + ATP12A 1 200.05 218.05
## + SLC26A4 1 200.05 218.05
## + TIA1 1 200.05 218.05
## - PPIA 1 207.68 221.68
## - ABCD3 1 208.34 222.34
## - DRD4 1 209.54 223.54
## - CACNG2 1 210.67 224.67
## - MPP3 1 211.72 225.72
## - GJA5 1 213.52 227.52
## - NEK2 1 225.45 239.45
##
## Step: AIC=212.12
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB
##
## Df Deviance AIC
## + HOXB5 1 189.26 209.26
## + DLG2 1 189.72 209.72
## + RPS6 1 189.97 209.97
## + PROX1 1 190.30 210.30
## + RPS20 1 190.50 210.50
## + SLC22A4 1 190.84 210.84
## + CACNA1C 1 191.18 211.18
## + NAP1L4 1 191.22 211.22
## + DUT 1 191.52 211.52
## + FH 1 191.78 211.78
## + GATA4 1 191.87 211.87
## + ADD1 1 191.87 211.87
## <none> 194.12 212.12
## + TLR1 1 192.14 212.14
## + NOL4 1 192.24 212.24
## + CLDN14 1 192.34 212.34
## + IRF3 1 192.37 212.37
## + RPS11 1 192.39 212.39
## + KLRB1 1 192.44 212.44
## + HDAC6 1 192.53 212.53
## + CLK3 1 192.57 212.57
## + CR1 1 192.60 212.60
## + BID 1 192.61 212.61
## + SPAG6 1 192.81 212.81
## + CDC42BPB 1 192.91 212.91
## + CYP39A1 1 193.01 213.01
## + ACADSB 1 193.02 213.02
## + ZNF202 1 193.03 213.03
## + PMAIP1 1 193.06 213.06
## + CRYBA1 1 193.14 213.14
## + RAB7L1 1 193.17 213.17
## + CD209 1 193.18 213.18
## + SHC3 1 193.21 213.21
## + KIR2DS3 1 193.21 213.21
## + OAZ3 1 193.27 213.27
## + HOXC10 1 193.31 213.31
## + LDHA 1 193.34 213.34
## + STAT3 1 193.35 213.35
## + BNIP2 1 193.38 213.38
## + UCP1 1 193.41 213.41
## + TFDP2 1 193.41 213.41
## + ADD2 1 193.41 213.41
## + TMEM2 1 193.46 213.46
## + ACTR3 1 193.47 213.47
## + FPR1 1 193.53 213.53
## + TGM3 1 193.54 213.54
## + CHST2 1 193.57 213.57
## + HNRPDL 1 193.66 213.66
## + PECI 1 193.67 213.67
## + ESR2 1 193.67 213.67
## + TGFBR2 1 193.69 213.69
## + GOT2 1 193.71 213.71
## + SRI 1 193.71 213.71
## + GGA1 1 193.74 213.74
## + JAK3 1 193.74 213.74
## + RFC5 1 193.78 213.78
## + SLC19A1 1 193.79 213.79
## + MMD 1 193.81 213.81
## + FGF6 1 193.84 213.84
## + ADCY8 1 193.85 213.85
## + CA11 1 193.87 213.87
## + HSD3B1 1 193.87 213.87
## + APRT 1 193.88 213.88
## + MGAM 1 193.89 213.89
## + ACADL 1 193.90 213.90
## + MME 1 193.91 213.91
## + ACYP1 1 193.93 213.93
## + TMOD2 1 193.96 213.96
## + TIA1 1 193.96 213.96
## + AGL 1 193.99 213.99
## + TNFRSF9 1 194.00 214.00
## + VPS35 1 194.01 214.01
## + B4GALT2 1 194.01 214.01
## + FCER1G 1 194.01 214.01
## + PBX1 1 194.02 214.02
## + SRD5A2 1 194.03 214.03
## + CLIC2 1 194.04 214.04
## + PDE7A 1 194.05 214.05
## + FBXW2 1 194.06 214.06
## + CAMK2B 1 194.07 214.07
## + ATP12A 1 194.08 214.08
## + SLC6A5 1 194.09 214.09
## + EWSR1 1 194.09 214.09
## + SLC26A4 1 194.09 214.09
## + CRK 1 194.10 214.10
## + MAP7 1 194.10 214.10
## + AXIN1 1 194.11 214.11
## + IFNA5 1 194.11 214.11
## + CDS1 1 194.12 214.12
## + SLC6A14 1 194.12 214.12
## + DOM3Z 1 194.12 214.12
## + NUP98 1 194.12 214.12
## + LARGE 1 194.12 214.12
## - CKB 1 200.05 216.05
## - PPIA 1 201.34 217.34
## - ABCD3 1 202.14 218.14
## - DRD4 1 203.68 219.68
## - MPP3 1 206.82 222.82
## - CACNG2 1 207.98 223.98
## - GJA5 1 208.37 224.37
## - NEK2 1 222.56 238.56
##
## Step: AIC=209.26
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5
##
## Df Deviance AIC
## + DLG2 1 184.81 206.81
## + RPS6 1 185.52 207.52
## + RPS20 1 185.63 207.63
## + CACNA1C 1 185.69 207.69
## + CLDN14 1 186.07 208.07
## + PROX1 1 186.07 208.07
## + NAP1L4 1 186.13 208.13
## + DUT 1 186.47 208.47
## + NOL4 1 186.50 208.50
## + TLR1 1 186.62 208.62
## + SLC22A4 1 186.71 208.71
## + GATA4 1 187.08 209.08
## <none> 189.26 209.26
## + CRYBA1 1 187.37 209.37
## + ADD1 1 187.49 209.49
## + BNIP2 1 187.53 209.53
## + BID 1 187.54 209.54
## + CYP39A1 1 187.56 209.56
## + KLRB1 1 187.62 209.62
## + CR1 1 187.66 209.66
## + CHST2 1 187.79 209.79
## + HOXC10 1 187.79 209.79
## + RAB7L1 1 187.80 209.80
## + FH 1 187.87 209.87
## + STAT3 1 187.89 209.89
## + IRF3 1 187.95 209.95
## + CLK3 1 188.02 210.02
## + SHC3 1 188.04 210.04
## + RPS11 1 188.06 210.06
## + HDAC6 1 188.11 210.11
## + ACTR3 1 188.13 210.13
## + TGM3 1 188.19 210.19
## + CDC42BPB 1 188.20 210.20
## + HNRPDL 1 188.21 210.21
## + FPR1 1 188.30 210.30
## + SRI 1 188.38 210.38
## + GGA1 1 188.39 210.39
## + TGFBR2 1 188.39 210.39
## + SPAG6 1 188.42 210.42
## + CD209 1 188.43 210.43
## + ACYP1 1 188.45 210.45
## + ZNF202 1 188.50 210.50
## + LDHA 1 188.51 210.51
## + GOT2 1 188.53 210.53
## + TIA1 1 188.54 210.54
## + ESR2 1 188.57 210.57
## + KIR2DS3 1 188.62 210.62
## + ACADL 1 188.62 210.62
## + ADCY8 1 188.62 210.62
## + ADD2 1 188.68 210.68
## + OAZ3 1 188.68 210.68
## + CA11 1 188.69 210.69
## + UCP1 1 188.74 210.74
## + TFDP2 1 188.74 210.74
## + PMAIP1 1 188.75 210.75
## + APRT 1 188.81 210.81
## + SLC19A1 1 188.83 210.83
## + ACADSB 1 188.91 210.91
## + EWSR1 1 188.96 210.96
## + TMEM2 1 188.96 210.96
## + TMOD2 1 189.01 211.01
## + AGL 1 189.02 211.02
## + MGAM 1 189.04 211.04
## + FCER1G 1 189.06 211.06
## + PECI 1 189.07 211.07
## + ATP12A 1 189.09 211.09
## + RFC5 1 189.11 211.11
## + MME 1 189.13 211.13
## + LARGE 1 189.13 211.13
## + FGF6 1 189.14 211.14
## + TNFRSF9 1 189.14 211.14
## + HSD3B1 1 189.14 211.14
## + SLC6A5 1 189.14 211.14
## + FBXW2 1 189.16 211.16
## + SRD5A2 1 189.19 211.19
## + MMD 1 189.19 211.19
## + CAMK2B 1 189.19 211.19
## + JAK3 1 189.19 211.19
## + CLIC2 1 189.20 211.20
## + MAP7 1 189.20 211.20
## + B4GALT2 1 189.21 211.21
## + DOM3Z 1 189.23 211.23
## + NUP98 1 189.25 211.25
## + PDE7A 1 189.25 211.25
## + CDS1 1 189.25 211.25
## + AXIN1 1 189.25 211.25
## + SLC26A4 1 189.25 211.25
## + PBX1 1 189.26 211.26
## + IFNA5 1 189.26 211.26
## + VPS35 1 189.26 211.26
## + SLC6A14 1 189.26 211.26
## + CRK 1 189.26 211.26
## - HOXB5 1 194.12 212.12
## - CKB 1 194.41 212.41
## - PPIA 1 196.03 214.03
## - DRD4 1 198.74 216.74
## - ABCD3 1 199.64 217.64
## - CACNG2 1 201.75 219.75
## - GJA5 1 204.35 222.35
## - MPP3 1 204.54 222.54
## - NEK2 1 214.69 232.69
##
## Step: AIC=206.81
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2
##
## Df Deviance AIC
## + SHC3 1 178.94 202.94
## + PROX1 1 181.00 205.00
## + RPS20 1 181.06 205.06
## + RPS6 1 181.28 205.28
## + CACNA1C 1 181.34 205.34
## + DUT 1 181.41 205.41
## + NAP1L4 1 181.60 205.60
## + TLR1 1 182.33 206.33
## + CDC42BPB 1 182.52 206.52
## + KLRB1 1 182.64 206.64
## + JAK3 1 182.66 206.66
## <none> 184.81 206.81
## + SLC22A4 1 182.83 206.83
## + CLDN14 1 182.88 206.88
## + HDAC6 1 182.89 206.89
## + NOL4 1 182.97 206.97
## + HOXC10 1 183.10 207.10
## + ADD1 1 183.24 207.24
## + RPS11 1 183.35 207.35
## + BNIP2 1 183.35 207.35
## + BID 1 183.38 207.38
## + FPR1 1 183.41 207.41
## + TGFBR2 1 183.42 207.42
## + CLK3 1 183.44 207.44
## + CR1 1 183.47 207.47
## + KIR2DS3 1 183.53 207.53
## + CHST2 1 183.55 207.55
## + GATA4 1 183.57 207.57
## + STAT3 1 183.60 207.60
## + ACTR3 1 183.64 207.64
## + SPAG6 1 183.67 207.67
## + CRYBA1 1 183.67 207.67
## + ADD2 1 183.77 207.77
## + RAB7L1 1 183.78 207.78
## + LDHA 1 183.82 207.82
## + HNRPDL 1 183.83 207.83
## + FH 1 184.01 208.01
## + CLIC2 1 184.03 208.03
## + GGA1 1 184.10 208.10
## + TFDP2 1 184.12 208.12
## + MME 1 184.13 208.13
## + ZNF202 1 184.14 208.14
## + SRI 1 184.18 208.18
## + UCP1 1 184.22 208.22
## + ACYP1 1 184.24 208.24
## + CA11 1 184.26 208.26
## + LARGE 1 184.27 208.27
## + PMAIP1 1 184.27 208.27
## + CYP39A1 1 184.28 208.28
## + TMEM2 1 184.29 208.29
## + GOT2 1 184.29 208.29
## + HSD3B1 1 184.29 208.29
## + RFC5 1 184.32 208.32
## + TIA1 1 184.33 208.33
## + IRF3 1 184.35 208.35
## + EWSR1 1 184.37 208.37
## + TGM3 1 184.41 208.41
## + SLC19A1 1 184.46 208.46
## + TMOD2 1 184.49 208.49
## + ATP12A 1 184.50 208.50
## + FCER1G 1 184.51 208.51
## + MGAM 1 184.54 208.54
## + SLC6A14 1 184.57 208.57
## + ACADL 1 184.58 208.58
## + TNFRSF9 1 184.61 208.61
## + MMD 1 184.62 208.62
## + CD209 1 184.64 208.64
## + APRT 1 184.66 208.66
## + ACADSB 1 184.66 208.66
## + CRK 1 184.69 208.69
## + ADCY8 1 184.70 208.70
## + ESR2 1 184.72 208.72
## + AGL 1 184.73 208.73
## + PECI 1 184.75 208.75
## + FBXW2 1 184.75 208.75
## + NUP98 1 184.76 208.76
## + PDE7A 1 184.76 208.76
## + SRD5A2 1 184.77 208.77
## + DOM3Z 1 184.77 208.77
## + AXIN1 1 184.77 208.77
## + IFNA5 1 184.78 208.78
## + PBX1 1 184.78 208.78
## + OAZ3 1 184.78 208.78
## + MAP7 1 184.78 208.78
## + VPS35 1 184.79 208.79
## + CAMK2B 1 184.79 208.79
## + B4GALT2 1 184.79 208.79
## + SLC26A4 1 184.81 208.81
## + FGF6 1 184.81 208.81
## + SLC6A5 1 184.81 208.81
## + CDS1 1 184.81 208.81
## - DLG2 1 189.26 209.26
## - CKB 1 189.59 209.59
## - HOXB5 1 189.72 209.72
## - DRD4 1 192.71 212.71
## - PPIA 1 192.72 212.72
## - ABCD3 1 196.51 216.51
## - CACNG2 1 199.40 219.40
## - MPP3 1 199.63 219.63
## - GJA5 1 202.40 222.40
## - NEK2 1 210.19 230.19
##
## Step: AIC=202.94
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3
##
## Df Deviance AIC
## + DUT 1 174.10 200.10
## + FPR1 1 174.45 200.45
## + CACNA1C 1 174.91 200.91
## + NAP1L4 1 175.24 201.24
## + PROX1 1 175.41 201.41
## + RPS6 1 175.69 201.69
## + TLR1 1 175.72 201.72
## + RPS20 1 175.77 201.77
## + SLC22A4 1 175.88 201.88
## + HOXC10 1 176.52 202.52
## + CLIC2 1 176.58 202.58
## + BID 1 176.75 202.75
## + HDAC6 1 176.80 202.80
## <none> 178.94 202.94
## + CLK3 1 177.13 203.13
## + ADD1 1 177.15 203.15
## + TGFBR2 1 177.18 203.18
## + UCP1 1 177.22 203.22
## + NOL4 1 177.25 203.25
## + CDC42BPB 1 177.42 203.42
## + CHST2 1 177.53 203.53
## + ACTR3 1 177.56 203.56
## + FCER1G 1 177.58 203.58
## + KIR2DS3 1 177.60 203.60
## + SPAG6 1 177.61 203.61
## + FH 1 177.74 203.74
## + KLRB1 1 177.80 203.80
## + LDHA 1 177.83 203.83
## + BNIP2 1 177.84 203.84
## + STAT3 1 177.85 203.85
## + RPS11 1 177.92 203.92
## + RAB7L1 1 177.96 203.96
## + TFDP2 1 178.00 204.00
## + CR1 1 178.01 204.01
## + MME 1 178.05 204.05
## + ADD2 1 178.10 204.10
## + RFC5 1 178.11 204.11
## + CYP39A1 1 178.11 204.11
## + SRI 1 178.18 204.18
## + JAK3 1 178.18 204.18
## + SLC6A5 1 178.20 204.20
## + TMEM2 1 178.35 204.35
## + GATA4 1 178.38 204.38
## + PMAIP1 1 178.45 204.45
## + TNFRSF9 1 178.46 204.46
## + CD209 1 178.46 204.46
## + CLDN14 1 178.47 204.47
## + EWSR1 1 178.47 204.47
## + HNRPDL 1 178.50 204.50
## + APRT 1 178.52 204.52
## + GOT2 1 178.62 204.62
## + HSD3B1 1 178.65 204.65
## + ACYP1 1 178.67 204.67
## + TIA1 1 178.68 204.68
## + IRF3 1 178.69 204.69
## + B4GALT2 1 178.72 204.72
## + FBXW2 1 178.73 204.73
## + ESR2 1 178.75 204.75
## + CA11 1 178.77 204.77
## + MGAM 1 178.78 204.78
## + CRYBA1 1 178.78 204.78
## + VPS35 1 178.81 204.81
## + GGA1 1 178.81 204.81
## + SLC26A4 1 178.81 204.81
## + CRK 1 178.82 204.82
## + TMOD2 1 178.83 204.83
## + ACADL 1 178.83 204.83
## + MMD 1 178.84 204.84
## + CDS1 1 178.85 204.85
## + FGF6 1 178.85 204.85
## + NUP98 1 178.86 204.86
## + ADCY8 1 178.86 204.86
## + DOM3Z 1 178.86 204.86
## + SRD5A2 1 178.87 204.87
## + PECI 1 178.87 204.87
## + CAMK2B 1 178.88 204.88
## + IFNA5 1 178.89 204.89
## + MAP7 1 178.89 204.89
## + ZNF202 1 178.90 204.90
## + AGL 1 178.91 204.91
## + ACADSB 1 178.91 204.91
## + AXIN1 1 178.92 204.92
## + ATP12A 1 178.92 204.92
## + SLC19A1 1 178.93 204.93
## + PBX1 1 178.93 204.93
## + LARGE 1 178.93 204.93
## + PDE7A 1 178.93 204.93
## + SLC6A14 1 178.93 204.93
## + TGM3 1 178.94 204.94
## + OAZ3 1 178.94 204.94
## - CKB 1 183.24 205.24
## - HOXB5 1 184.43 206.43
## - SHC3 1 184.81 206.81
## - DRD4 1 185.55 207.55
## - PPIA 1 185.77 207.77
## - DLG2 1 188.04 210.04
## - ABCD3 1 189.47 211.47
## - MPP3 1 193.51 215.51
## - CACNG2 1 194.78 216.78
## - GJA5 1 198.09 220.09
## - NEK2 1 204.76 226.76
##
## Step: AIC=200.1
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT
##
## Df Deviance AIC
## + RPS6 1 170.12 198.12
## + SLC22A4 1 170.47 198.47
## + RPS20 1 170.48 198.48
## + CACNA1C 1 170.50 198.50
## + FPR1 1 170.80 198.80
## + BID 1 170.90 198.90
## + NAP1L4 1 171.26 199.26
## + TLR1 1 171.41 199.41
## + HOXC10 1 171.55 199.55
## + RPS11 1 172.03 200.03
## + STAT3 1 172.03 200.03
## + PROX1 1 172.06 200.06
## <none> 174.10 200.10
## + CHST2 1 172.11 200.11
## + UCP1 1 172.17 200.17
## + ADD1 1 172.23 200.23
## + NOL4 1 172.28 200.28
## + TGFBR2 1 172.33 200.33
## + TFDP2 1 172.36 200.36
## + CLIC2 1 172.42 200.42
## + RAB7L1 1 172.50 200.50
## + HDAC6 1 172.52 200.52
## + KLRB1 1 172.54 200.54
## + ACTR3 1 172.57 200.57
## + CLDN14 1 172.69 200.69
## + CR1 1 172.72 200.72
## + BNIP2 1 172.78 200.78
## + CLK3 1 172.81 200.81
## + ADD2 1 172.83 200.83
## + MME 1 172.98 200.98
## + TMEM2 1 173.07 201.07
## + JAK3 1 173.16 201.16
## + FH 1 173.17 201.17
## + SRI 1 173.18 201.18
## + GATA4 1 173.19 201.19
## + ACYP1 1 173.32 201.32
## + FCER1G 1 173.35 201.35
## + SPAG6 1 173.36 201.36
## + EWSR1 1 173.39 201.39
## + CYP39A1 1 173.43 201.43
## + LDHA 1 173.61 201.61
## + HSD3B1 1 173.66 201.66
## + KIR2DS3 1 173.66 201.66
## + CDC42BPB 1 173.67 201.67
## + GGA1 1 173.69 201.69
## + PMAIP1 1 173.71 201.71
## + CD209 1 173.71 201.71
## + CRYBA1 1 173.72 201.72
## + HNRPDL 1 173.77 201.77
## + PBX1 1 173.80 201.80
## + ACADL 1 173.87 201.87
## + RFC5 1 173.88 201.88
## + FBXW2 1 173.89 201.89
## + B4GALT2 1 173.89 201.89
## + SLC6A5 1 173.95 201.95
## + TGM3 1 173.96 201.96
## + ADCY8 1 173.99 201.99
## + AXIN1 1 174.00 202.00
## + IRF3 1 174.01 202.01
## + LARGE 1 174.01 202.01
## + APRT 1 174.02 202.02
## + SLC26A4 1 174.02 202.02
## + MGAM 1 174.03 202.03
## + FGF6 1 174.03 202.03
## + CDS1 1 174.03 202.03
## + TIA1 1 174.04 202.04
## + TNFRSF9 1 174.05 202.05
## + DOM3Z 1 174.06 202.06
## + VPS35 1 174.06 202.06
## + GOT2 1 174.08 202.08
## + OAZ3 1 174.08 202.08
## + CA11 1 174.08 202.08
## + ATP12A 1 174.09 202.09
## + IFNA5 1 174.09 202.09
## + CAMK2B 1 174.09 202.09
## + CRK 1 174.09 202.09
## + SLC19A1 1 174.09 202.09
## + PECI 1 174.09 202.09
## + PDE7A 1 174.09 202.09
## + SLC6A14 1 174.10 202.10
## + MMD 1 174.10 202.10
## + TMOD2 1 174.10 202.10
## + ESR2 1 174.10 202.10
## + SRD5A2 1 174.10 202.10
## + ACADSB 1 174.10 202.10
## + NUP98 1 174.10 202.10
## + AGL 1 174.10 202.10
## + MAP7 1 174.10 202.10
## + ZNF202 1 174.10 202.10
## - CKB 1 178.20 202.20
## - DUT 1 178.94 202.94
## - HOXB5 1 179.62 203.62
## - PPIA 1 180.48 204.48
## - SHC3 1 181.41 205.41
## - DRD4 1 182.10 206.10
## - DLG2 1 185.08 209.08
## - MPP3 1 186.67 210.67
## - ABCD3 1 187.25 211.25
## - GJA5 1 189.07 213.07
## - NEK2 1 189.94 213.94
## - CACNG2 1 190.50 214.50
##
## Step: AIC=198.11
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6
##
## Df Deviance AIC
## + SLC22A4 1 166.15 196.15
## + CACNA1C 1 166.75 196.75
## + TLR1 1 166.87 196.87
## + FPR1 1 167.08 197.08
## + HOXC10 1 167.37 197.37
## + PROX1 1 167.49 197.49
## + NAP1L4 1 167.93 197.93
## + STAT3 1 167.94 197.94
## <none> 170.12 198.12
## + ADD2 1 168.19 198.19
## + BID 1 168.28 198.28
## + BNIP2 1 168.33 198.33
## + UCP1 1 168.37 198.37
## + TGFBR2 1 168.45 198.45
## + CLDN14 1 168.56 198.56
## + FCER1G 1 168.58 198.58
## + CHST2 1 168.58 198.58
## + JAK3 1 168.64 198.64
## + CLIC2 1 168.73 198.73
## + TFDP2 1 168.76 198.76
## + CR1 1 168.80 198.80
## + KLRB1 1 168.80 198.80
## + EWSR1 1 168.83 198.83
## + RAB7L1 1 168.86 198.86
## + MME 1 168.94 198.94
## + GATA4 1 168.94 198.94
## + HDAC6 1 169.05 199.05
## + CLK3 1 169.05 199.05
## + KIR2DS3 1 169.06 199.06
## + NOL4 1 169.11 199.11
## + ADD1 1 169.31 199.31
## + TMEM2 1 169.33 199.33
## + ACTR3 1 169.35 199.35
## + LDHA 1 169.43 199.43
## + FH 1 169.44 199.44
## + SPAG6 1 169.47 199.47
## + RPS20 1 169.52 199.52
## + HNRPDL 1 169.60 199.60
## + HSD3B1 1 169.60 199.60
## + RPS11 1 169.64 199.64
## + ACYP1 1 169.64 199.64
## + CRYBA1 1 169.67 199.67
## + GGA1 1 169.73 199.73
## + LARGE 1 169.75 199.75
## + SLC6A14 1 169.77 199.77
## + SRI 1 169.80 199.80
## + CDS1 1 169.85 199.85
## + ACADL 1 169.88 199.88
## + MGAM 1 169.92 199.92
## + SLC6A5 1 169.93 199.93
## + CDC42BPB 1 169.94 199.94
## + PMAIP1 1 169.96 199.96
## + B4GALT2 1 169.97 199.97
## + AXIN1 1 169.98 199.98
## + MAP7 1 169.98 199.98
## + CD209 1 169.99 199.99
## + RFC5 1 170.00 200.00
## + APRT 1 170.00 200.00
## + PBX1 1 170.00 200.00
## + ADCY8 1 170.01 200.01
## + SLC26A4 1 170.01 200.01
## + ATP12A 1 170.03 200.03
## + FGF6 1 170.05 200.05
## + PDE7A 1 170.06 200.06
## + TNFRSF9 1 170.07 200.07
## + CYP39A1 1 170.07 200.07
## + PECI 1 170.08 200.08
## + FBXW2 1 170.08 200.08
## + OAZ3 1 170.09 200.09
## + SRD5A2 1 170.09 200.09
## + IRF3 1 170.09 200.09
## + CRK 1 170.09 200.09
## - RPS6 1 174.10 200.10
## + TGM3 1 170.10 200.10
## + IFNA5 1 170.11 200.11
## + CAMK2B 1 170.11 200.11
## + SLC19A1 1 170.11 200.11
## + ZNF202 1 170.11 200.11
## + TMOD2 1 170.11 200.11
## + DOM3Z 1 170.11 200.11
## + MMD 1 170.11 200.11
## + CA11 1 170.11 200.11
## + NUP98 1 170.11 200.11
## + TIA1 1 170.11 200.11
## + ACADSB 1 170.11 200.11
## + ESR2 1 170.11 200.11
## + AGL 1 170.11 200.11
## + VPS35 1 170.12 200.12
## + GOT2 1 170.12 200.12
## - HOXB5 1 175.47 201.47
## - CKB 1 175.58 201.58
## - DUT 1 175.69 201.69
## - PPIA 1 176.12 202.12
## - SHC3 1 177.00 203.00
## - DRD4 1 177.96 203.96
## - DLG2 1 180.89 206.89
## - MPP3 1 181.92 207.92
## - GJA5 1 182.63 208.63
## - ABCD3 1 183.13 209.13
## - NEK2 1 183.26 209.26
## - CACNG2 1 185.99 211.99
##
## Step: AIC=196.14
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4
##
## Df Deviance AIC
## + PROX1 1 162.51 194.51
## + FPR1 1 162.69 194.69
## + CACNA1C 1 163.01 195.01
## + HOXC10 1 163.25 195.25
## + STAT3 1 163.38 195.38
## + BID 1 163.57 195.57
## + NAP1L4 1 163.70 195.70
## + ADD2 1 163.84 195.84
## + JAK3 1 163.90 195.90
## + KLRB1 1 163.93 195.93
## + TLR1 1 163.96 195.96
## + GATA4 1 164.12 196.12
## <none> 166.15 196.15
## + BNIP2 1 164.16 196.16
## + TGFBR2 1 164.42 196.42
## + ACTR3 1 164.48 196.48
## + KIR2DS3 1 164.51 196.51
## + HDAC6 1 164.64 196.64
## + CHST2 1 164.72 196.72
## + ADD1 1 164.72 196.72
## + CDC42BPB 1 164.85 196.85
## + CLIC2 1 164.99 196.99
## + TMEM2 1 165.04 197.04
## + NOL4 1 165.06 197.06
## + LDHA 1 165.14 197.14
## + CR1 1 165.16 197.16
## + TFDP2 1 165.17 197.17
## + CLK3 1 165.24 197.24
## + CLDN14 1 165.52 197.52
## + RAB7L1 1 165.52 197.52
## + MME 1 165.52 197.52
## + EWSR1 1 165.52 197.52
## + FCER1G 1 165.60 197.60
## + OAZ3 1 165.61 197.61
## + PBX1 1 165.63 197.63
## + RPS20 1 165.66 197.66
## + ACADL 1 165.66 197.66
## + RPS11 1 165.67 197.67
## + ADCY8 1 165.78 197.78
## + FH 1 165.82 197.82
## + CRYBA1 1 165.83 197.83
## + HNRPDL 1 165.83 197.83
## + ACYP1 1 165.85 197.85
## + SPAG6 1 165.85 197.85
## + B4GALT2 1 165.86 197.86
## + HSD3B1 1 165.91 197.91
## + SLC6A5 1 165.91 197.91
## - CKB 1 169.92 197.92
## + GGA1 1 165.93 197.93
## + PMAIP1 1 165.93 197.93
## + RFC5 1 165.93 197.93
## + MAP7 1 165.94 197.94
## + CDS1 1 165.96 197.96
## + SRI 1 165.96 197.96
## + ACADSB 1 165.97 197.97
## + IRF3 1 165.97 197.97
## + NUP98 1 165.98 197.98
## + TMOD2 1 165.99 197.99
## + TNFRSF9 1 165.99 197.99
## + TIA1 1 166.01 198.01
## + UCP1 1 166.03 198.03
## + CAMK2B 1 166.03 198.03
## + AGL 1 166.03 198.03
## + LARGE 1 166.07 198.07
## + ZNF202 1 166.09 198.09
## + SRD5A2 1 166.09 198.09
## + SLC26A4 1 166.09 198.09
## + PECI 1 166.10 198.10
## + PDE7A 1 166.10 198.10
## + FBXW2 1 166.11 198.11
## + AXIN1 1 166.11 198.11
## - SLC22A4 1 170.12 198.12
## + FGF6 1 166.12 198.12
## + CYP39A1 1 166.12 198.12
## + MGAM 1 166.12 198.12
## + SLC6A14 1 166.12 198.12
## + SLC19A1 1 166.13 198.13
## + CRK 1 166.13 198.13
## + CD209 1 166.13 198.13
## + DOM3Z 1 166.13 198.13
## + VPS35 1 166.14 198.14
## + GOT2 1 166.14 198.14
## + ATP12A 1 166.14 198.14
## + ESR2 1 166.14 198.14
## + APRT 1 166.14 198.14
## + TGM3 1 166.14 198.14
## + CA11 1 166.14 198.14
## + MMD 1 166.14 198.14
## + IFNA5 1 166.15 198.15
## - RPS6 1 170.47 198.47
## - HOXB5 1 170.60 198.60
## - DRD4 1 171.32 199.32
## - PPIA 1 171.66 199.66
## - DUT 1 172.32 200.32
## - SHC3 1 174.95 202.95
## - DLG2 1 176.39 204.39
## - NEK2 1 176.78 204.78
## - MPP3 1 177.04 205.04
## - ABCD3 1 177.68 205.68
## - GJA5 1 179.59 207.59
## - CACNG2 1 180.04 208.04
##
## Step: AIC=194.51
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1
##
## Df Deviance AIC
## + TLR1 1 157.83 191.83
## + BID 1 158.74 192.74
## + FPR1 1 159.07 193.07
## + KLRB1 1 159.15 193.15
## + ADD2 1 159.33 193.33
## + BNIP2 1 159.42 193.42
## + HOXC10 1 159.52 193.52
## + NAP1L4 1 159.52 193.52
## + GATA4 1 159.70 193.70
## + JAK3 1 159.71 193.71
## + CHST2 1 159.82 193.82
## + NOL4 1 160.12 194.12
## + CACNA1C 1 160.20 194.20
## <none> 162.51 194.51
## + TFDP2 1 160.59 194.59
## + RAB7L1 1 160.61 194.61
## + STAT3 1 160.62 194.62
## + ACTR3 1 160.71 194.71
## + TMEM2 1 160.99 194.99
## + HDAC6 1 161.05 195.05
## + CLIC2 1 161.22 195.22
## + ADD1 1 161.23 195.23
## + LDHA 1 161.32 195.32
## + CR1 1 161.33 195.33
## + TGFBR2 1 161.38 195.38
## + FCER1G 1 161.55 195.55
## + CLK3 1 161.60 195.60
## + ACADL 1 161.67 195.67
## + CDC42BPB 1 161.67 195.67
## + MME 1 161.76 195.76
## + PBX1 1 161.82 195.82
## + KIR2DS3 1 161.83 195.83
## + RPS20 1 161.85 195.85
## + TIA1 1 161.86 195.86
## + CRYBA1 1 161.88 195.88
## + OAZ3 1 161.88 195.88
## + EWSR1 1 161.95 195.95
## + RPS11 1 161.98 195.98
## + ACADSB 1 162.06 196.06
## - PROX1 1 166.15 196.15
## + FH 1 162.18 196.18
## + AGL 1 162.21 196.21
## + HSD3B1 1 162.21 196.21
## + ADCY8 1 162.23 196.23
## + CLDN14 1 162.23 196.23
## + HNRPDL 1 162.23 196.23
## + FBXW2 1 162.24 196.24
## + ACYP1 1 162.26 196.26
## + AXIN1 1 162.27 196.27
## + MAP7 1 162.28 196.28
## + SLC6A14 1 162.29 196.29
## + SRI 1 162.31 196.31
## + CRK 1 162.32 196.32
## + SLC26A4 1 162.33 196.33
## + CD209 1 162.33 196.33
## + B4GALT2 1 162.35 196.35
## + CDS1 1 162.36 196.36
## + ATP12A 1 162.38 196.38
## + SRD5A2 1 162.38 196.38
## + UCP1 1 162.38 196.38
## + TNFRSF9 1 162.38 196.38
## + GGA1 1 162.41 196.41
## + ESR2 1 162.44 196.44
## + SPAG6 1 162.44 196.44
## + IFNA5 1 162.46 196.46
## + PMAIP1 1 162.46 196.46
## + SLC6A5 1 162.47 196.47
## + MGAM 1 162.47 196.47
## + SLC19A1 1 162.49 196.49
## + IRF3 1 162.49 196.49
## + TMOD2 1 162.49 196.49
## + CYP39A1 1 162.49 196.49
## + TGM3 1 162.49 196.49
## + PDE7A 1 162.50 196.50
## + CA11 1 162.50 196.50
## + ZNF202 1 162.50 196.50
## + LARGE 1 162.50 196.50
## + NUP98 1 162.50 196.50
## + APRT 1 162.50 196.50
## + MMD 1 162.51 196.51
## + FGF6 1 162.51 196.51
## + VPS35 1 162.51 196.51
## + CAMK2B 1 162.51 196.51
## + DOM3Z 1 162.51 196.51
## + GOT2 1 162.51 196.51
## + RFC5 1 162.51 196.51
## + PECI 1 162.51 196.51
## - DUT 1 166.64 196.64
## - HOXB5 1 166.82 196.82
## - DRD4 1 167.18 197.18
## - RPS6 1 167.30 197.30
## - SLC22A4 1 167.49 197.49
## - CKB 1 167.50 197.50
## - PPIA 1 168.55 198.55
## - SHC3 1 170.69 200.69
## - DLG2 1 173.14 203.14
## - NEK2 1 174.00 204.00
## - GJA5 1 175.50 205.50
## - CACNG2 1 175.53 205.53
## - ABCD3 1 175.65 205.65
## - MPP3 1 176.91 206.91
##
## Step: AIC=191.83
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1 +
## TLR1
##
## Df Deviance AIC
## + BID 1 153.72 189.72
## + ADD2 1 155.29 191.29
## + GATA4 1 155.34 191.34
## + TGFBR2 1 155.54 191.54
## <none> 157.83 191.83
## + STAT3 1 155.91 191.91
## + NAP1L4 1 156.09 192.09
## + HOXC10 1 156.18 192.18
## + TFDP2 1 156.25 192.25
## + JAK3 1 156.31 192.31
## + CACNA1C 1 156.32 192.32
## + FPR1 1 156.52 192.52
## + BNIP2 1 156.56 192.56
## + LDHA 1 156.57 192.57
## - DUT 1 160.64 192.64
## + KLRB1 1 156.67 192.67
## + CLK3 1 156.71 192.71
## + NOL4 1 156.75 192.75
## + ADD1 1 156.80 192.80
## + ACADL 1 156.80 192.80
## + HDAC6 1 156.81 192.81
## + MME 1 156.84 192.84
## + ACTR3 1 156.86 192.86
## + TMEM2 1 156.91 192.91
## + RAB7L1 1 156.97 192.97
## + CDS1 1 157.02 193.02
## + KIR2DS3 1 157.04 193.04
## + TIA1 1 157.13 193.13
## + CHST2 1 157.14 193.14
## + B4GALT2 1 157.14 193.14
## + RPS11 1 157.20 193.20
## + ACYP1 1 157.26 193.26
## + FH 1 157.30 193.30
## + AGL 1 157.31 193.31
## + CDC42BPB 1 157.36 193.36
## + GOT2 1 157.37 193.37
## + CR1 1 157.41 193.41
## + FBXW2 1 157.42 193.42
## + RPS20 1 157.44 193.44
## + EWSR1 1 157.47 193.47
## + CLIC2 1 157.48 193.48
## + UCP1 1 157.51 193.51
## + OAZ3 1 157.52 193.52
## + HSD3B1 1 157.53 193.53
## + SLC26A4 1 157.55 193.55
## + CRK 1 157.56 193.56
## + PBX1 1 157.61 193.61
## + MGAM 1 157.64 193.64
## + TMOD2 1 157.68 193.68
## + PMAIP1 1 157.68 193.68
## + HNRPDL 1 157.68 193.68
## + CLDN14 1 157.69 193.69
## + PDE7A 1 157.71 193.71
## + DOM3Z 1 157.71 193.71
## + ACADSB 1 157.71 193.71
## + SPAG6 1 157.72 193.72
## + MAP7 1 157.73 193.73
## + CD209 1 157.73 193.73
## + SRI 1 157.74 193.74
## + SRD5A2 1 157.76 193.76
## + CRYBA1 1 157.78 193.78
## + CA11 1 157.78 193.78
## + NUP98 1 157.79 193.79
## + ESR2 1 157.80 193.80
## + SLC6A14 1 157.80 193.80
## + CYP39A1 1 157.80 193.80
## - SLC22A4 1 161.80 193.80
## + TNFRSF9 1 157.80 193.80
## + SLC6A5 1 157.80 193.80
## + IRF3 1 157.81 193.81
## + APRT 1 157.81 193.81
## + ATP12A 1 157.81 193.81
## + FCER1G 1 157.81 193.81
## + TGM3 1 157.81 193.81
## + ZNF202 1 157.81 193.81
## + IFNA5 1 157.82 193.82
## + MMD 1 157.82 193.82
## + RFC5 1 157.82 193.82
## + GGA1 1 157.82 193.82
## + PECI 1 157.82 193.82
## + ADCY8 1 157.82 193.82
## + AXIN1 1 157.82 193.82
## + VPS35 1 157.83 193.83
## + FGF6 1 157.83 193.83
## + CAMK2B 1 157.83 193.83
## + LARGE 1 157.83 193.83
## + SLC19A1 1 157.83 193.83
## - DRD4 1 162.19 194.19
## - CKB 1 162.41 194.41
## - TLR1 1 162.51 194.51
## - HOXB5 1 162.72 194.72
## - RPS6 1 163.59 195.59
## - PROX1 1 163.96 195.96
## - PPIA 1 165.90 197.90
## - SHC3 1 166.85 198.85
## - DLG2 1 168.34 200.34
## - CACNG2 1 170.98 202.98
## - NEK2 1 172.05 204.05
## - MPP3 1 172.90 204.90
## - GJA5 1 174.71 206.71
## - ABCD3 1 175.10 207.10
##
## Step: AIC=189.72
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1 +
## TLR1 + BID
##
## Df Deviance AIC
## + STAT3 1 151.65 189.65
## <none> 153.72 189.72
## + NAP1L4 1 151.74 189.74
## + LDHA 1 151.86 189.86
## + TGFBR2 1 151.86 189.86
## + ADD2 1 151.89 189.89
## + TMEM2 1 152.05 190.05
## + CLK3 1 152.06 190.06
## + TFDP2 1 152.12 190.12
## + RAB7L1 1 152.18 190.18
## + GATA4 1 152.47 190.47
## + MME 1 152.48 190.48
## + KLRB1 1 152.50 190.50
## + SLC26A4 1 152.50 190.50
## + FH 1 152.55 190.55
## + ACADL 1 152.63 190.63
## + CDS1 1 152.71 190.71
## + JAK3 1 152.78 190.78
## + FBXW2 1 152.80 190.80
## + FPR1 1 152.83 190.83
## + NOL4 1 152.85 190.85
## + CACNA1C 1 152.88 190.88
## + HDAC6 1 152.88 190.88
## + KIR2DS3 1 152.92 190.92
## + ADD1 1 152.92 190.92
## + BNIP2 1 152.94 190.94
## + HOXC10 1 152.95 190.95
## - DUT 1 156.97 190.97
## + GOT2 1 153.00 191.00
## + UCP1 1 153.21 191.21
## + CLIC2 1 153.24 191.24
## + AGL 1 153.27 191.27
## + PDE7A 1 153.33 191.33
## + CR1 1 153.35 191.35
## + CRK 1 153.36 191.36
## + ACTR3 1 153.37 191.37
## + TMOD2 1 153.38 191.38
## - RPS6 1 157.40 191.40
## + FGF6 1 153.40 191.40
## + RPS11 1 153.40 191.40
## + TGM3 1 153.43 191.43
## + TIA1 1 153.44 191.44
## + ACYP1 1 153.46 191.46
## + EWSR1 1 153.48 191.48
## + OAZ3 1 153.49 191.49
## + HSD3B1 1 153.49 191.49
## + CHST2 1 153.52 191.52
## - DRD4 1 157.52 191.52
## + LARGE 1 153.56 191.56
## + PECI 1 153.56 191.56
## + MAP7 1 153.56 191.56
## + B4GALT2 1 153.57 191.57
## + CA11 1 153.59 191.59
## + CDC42BPB 1 153.59 191.59
## + RPS20 1 153.59 191.59
## + APRT 1 153.59 191.59
## + GGA1 1 153.59 191.59
## + HNRPDL 1 153.59 191.59
## + MGAM 1 153.60 191.60
## + IFNA5 1 153.61 191.61
## + TNFRSF9 1 153.61 191.61
## + RFC5 1 153.62 191.62
## + PMAIP1 1 153.63 191.63
## + SRD5A2 1 153.64 191.64
## + SLC6A14 1 153.66 191.66
## + MMD 1 153.66 191.66
## + CLDN14 1 153.67 191.67
## + FCER1G 1 153.67 191.67
## + CAMK2B 1 153.67 191.67
## + ADCY8 1 153.68 191.68
## + VPS35 1 153.68 191.68
## + ATP12A 1 153.69 191.69
## + DOM3Z 1 153.69 191.69
## + ESR2 1 153.69 191.69
## + AXIN1 1 153.71 191.71
## + ACADSB 1 153.71 191.71
## + CD209 1 153.71 191.71
## + IRF3 1 153.72 191.72
## + SPAG6 1 153.72 191.72
## + ZNF202 1 153.72 191.72
## + NUP98 1 153.72 191.72
## + SRI 1 153.72 191.72
## + SLC19A1 1 153.72 191.72
## + PBX1 1 153.72 191.72
## + CYP39A1 1 153.72 191.72
## + SLC6A5 1 153.72 191.72
## + CRYBA1 1 153.72 191.72
## - CKB 1 157.80 191.80
## - BID 1 157.83 191.83
## - SLC22A4 1 158.54 192.54
## - HOXB5 1 158.69 192.69
## - TLR1 1 158.74 192.74
## - PROX1 1 161.36 195.36
## - DLG2 1 163.96 197.96
## - PPIA 1 164.60 198.60
## - SHC3 1 164.63 198.63
## - NEK2 1 168.63 202.63
## - CACNG2 1 169.04 203.04
## - MPP3 1 169.84 203.84
## - ABCD3 1 173.21 207.21
## - GJA5 1 173.71 207.71
##
## Step: AIC=189.65
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1 +
## TLR1 + BID + STAT3
##
## Df Deviance AIC
## + FH 1 149.63 189.63
## <none> 151.65 189.65
## + NAP1L4 1 149.66 189.66
## + RAB7L1 1 149.69 189.69
## - STAT3 1 153.72 189.72
## + TFDP2 1 149.86 189.86
## + CLK3 1 149.86 189.86
## + LDHA 1 149.97 189.97
## + TGFBR2 1 150.05 190.05
## + TMEM2 1 150.06 190.06
## + ADD2 1 150.14 190.14
## + MME 1 150.31 190.31
## + SLC26A4 1 150.44 190.44
## + KIR2DS3 1 150.57 190.57
## + JAK3 1 150.61 190.61
## + GATA4 1 150.67 190.67
## + HOXC10 1 150.69 190.69
## + FPR1 1 150.70 190.70
## + FBXW2 1 150.73 190.73
## + CACNA1C 1 150.84 190.84
## + NOL4 1 150.84 190.84
## + UCP1 1 150.88 190.88
## + CR1 1 151.00 191.00
## + B4GALT2 1 151.03 191.03
## + GOT2 1 151.05 191.05
## + ACADL 1 151.05 191.05
## + FGF6 1 151.08 191.08
## + CDS1 1 151.09 191.09
## + KLRB1 1 151.11 191.11
## - DRD4 1 155.15 191.15
## + CRK 1 151.15 191.15
## + BNIP2 1 151.22 191.22
## + HDAC6 1 151.24 191.24
## + HSD3B1 1 151.25 191.25
## + TGM3 1 151.27 191.27
## + ADD1 1 151.35 191.35
## + MMD 1 151.37 191.37
## + MAP7 1 151.42 191.42
## + PDE7A 1 151.42 191.42
## - RPS6 1 155.42 191.42
## + CLIC2 1 151.43 191.43
## + AGL 1 151.43 191.43
## + CHST2 1 151.44 191.44
## + EWSR1 1 151.44 191.44
## + AXIN1 1 151.45 191.45
## + TMOD2 1 151.46 191.46
## + RFC5 1 151.48 191.48
## + LARGE 1 151.49 191.49
## + RPS11 1 151.49 191.49
## + PECI 1 151.51 191.51
## + TIA1 1 151.54 191.54
## + OAZ3 1 151.54 191.54
## + IRF3 1 151.54 191.54
## + ZNF202 1 151.54 191.54
## + GGA1 1 151.56 191.56
## + ESR2 1 151.56 191.56
## + CAMK2B 1 151.57 191.57
## + ACTR3 1 151.57 191.57
## + CDC42BPB 1 151.57 191.57
## + TNFRSF9 1 151.58 191.58
## + CA11 1 151.58 191.58
## + ACYP1 1 151.59 191.59
## + IFNA5 1 151.59 191.59
## + RPS20 1 151.59 191.59
## + PMAIP1 1 151.59 191.59
## + ADCY8 1 151.59 191.59
## + SLC6A14 1 151.60 191.60
## + SRD5A2 1 151.61 191.61
## + CLDN14 1 151.61 191.61
## + HNRPDL 1 151.61 191.61
## + ATP12A 1 151.62 191.62
## + SPAG6 1 151.63 191.63
## + CRYBA1 1 151.63 191.63
## + PBX1 1 151.63 191.63
## + SRI 1 151.64 191.64
## + SLC19A1 1 151.64 191.64
## + NUP98 1 151.64 191.64
## + DOM3Z 1 151.64 191.64
## + CD209 1 151.64 191.64
## + ACADSB 1 151.64 191.64
## + FCER1G 1 151.64 191.64
## + VPS35 1 151.64 191.64
## + CYP39A1 1 151.64 191.64
## + MGAM 1 151.65 191.65
## + SLC6A5 1 151.65 191.65
## + APRT 1 151.65 191.65
## - DUT 1 155.82 191.82
## - CKB 1 155.90 191.90
## - BID 1 155.91 191.91
## - SLC22A4 1 156.65 192.65
## - TLR1 1 156.73 192.73
## - HOXB5 1 157.06 193.06
## - PROX1 1 157.98 193.98
## - DLG2 1 161.91 197.91
## - SHC3 1 162.23 198.23
## - PPIA 1 163.18 199.18
## - NEK2 1 166.84 202.84
## - MPP3 1 167.17 203.17
## - CACNG2 1 168.41 204.41
## - ABCD3 1 168.63 204.63
## - GJA5 1 171.87 207.87
##
## Step: AIC=189.63
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1 +
## TLR1 + BID + STAT3 + FH
##
## Df Deviance AIC
## + LDHA 1 147.34 189.34
## + CLK3 1 147.36 189.36
## + TMEM2 1 147.38 189.38
## <none> 149.63 189.63
## - FH 1 151.65 189.65
## + NAP1L4 1 147.86 189.86
## + TFDP2 1 147.98 189.98
## + MME 1 148.13 190.13
## + TGM3 1 148.38 190.38
## + TGFBR2 1 148.47 190.47
## + SLC26A4 1 148.47 190.47
## + CR1 1 148.47 190.47
## - STAT3 1 152.55 190.55
## + CACNA1C 1 148.58 190.58
## + B4GALT2 1 148.60 190.60
## + KIR2DS3 1 148.61 190.61
## + ADD2 1 148.64 190.64
## + RAB7L1 1 148.66 190.66
## - RPS6 1 152.69 190.69
## + HOXC10 1 148.76 190.76
## + FBXW2 1 148.87 190.87
## + JAK3 1 148.91 190.91
## + UCP1 1 148.91 190.91
## + FPR1 1 148.94 190.94
## + KLRB1 1 148.98 190.98
## + NOL4 1 149.04 191.04
## + FGF6 1 149.08 191.08
## + HSD3B1 1 149.08 191.08
## + GATA4 1 149.15 191.15
## + RPS11 1 149.18 191.18
## + CDS1 1 149.20 191.20
## + HDAC6 1 149.24 191.24
## + RPS20 1 149.25 191.25
## + CLIC2 1 149.28 191.28
## + ADD1 1 149.29 191.29
## - DRD4 1 153.30 191.30
## + ESR2 1 149.32 191.32
## + SRD5A2 1 149.33 191.33
## + TMOD2 1 149.34 191.34
## + AXIN1 1 149.37 191.37
## + AGL 1 149.38 191.38
## + ADCY8 1 149.39 191.39
## + CRK 1 149.40 191.40
## + GOT2 1 149.41 191.41
## + CA11 1 149.44 191.44
## + ACADL 1 149.44 191.44
## + LARGE 1 149.45 191.45
## + MMD 1 149.46 191.46
## + PDE7A 1 149.47 191.47
## + CRYBA1 1 149.47 191.47
## + TNFRSF9 1 149.47 191.47
## + BNIP2 1 149.48 191.48
## + OAZ3 1 149.48 191.48
## + HNRPDL 1 149.48 191.48
## + IFNA5 1 149.48 191.48
## + SLC6A14 1 149.51 191.51
## + FCER1G 1 149.53 191.53
## + CLDN14 1 149.53 191.53
## + CAMK2B 1 149.54 191.54
## + IRF3 1 149.55 191.55
## + NUP98 1 149.55 191.55
## + CDC42BPB 1 149.56 191.56
## + PECI 1 149.56 191.56
## + ZNF202 1 149.56 191.56
## + DOM3Z 1 149.57 191.57
## + VPS35 1 149.57 191.57
## + CHST2 1 149.58 191.58
## + EWSR1 1 149.58 191.58
## + ACYP1 1 149.58 191.58
## + RFC5 1 149.59 191.59
## + MGAM 1 149.60 191.60
## + ATP12A 1 149.61 191.61
## + CYP39A1 1 149.61 191.61
## + PMAIP1 1 149.62 191.62
## + SRI 1 149.62 191.62
## + PBX1 1 149.62 191.62
## + TIA1 1 149.62 191.62
## + SPAG6 1 149.62 191.62
## + GGA1 1 149.62 191.62
## + APRT 1 149.62 191.62
## + SLC6A5 1 149.63 191.63
## + SLC19A1 1 149.63 191.63
## + MAP7 1 149.63 191.63
## + CD209 1 149.63 191.63
## + ACADSB 1 149.63 191.63
## + ACTR3 1 149.63 191.63
## - DUT 1 153.77 191.77
## - SLC22A4 1 153.96 191.96
## - CKB 1 154.27 192.27
## - HOXB5 1 154.35 192.35
## - BID 1 154.84 192.84
## - TLR1 1 155.20 193.20
## - PROX1 1 156.04 194.04
## - DLG2 1 158.97 196.97
## - SHC3 1 160.84 198.84
## - PPIA 1 162.67 200.67
## - MPP3 1 165.09 203.09
## - NEK2 1 166.60 204.60
## - ABCD3 1 167.55 205.55
## - CACNG2 1 167.93 205.93
## - GJA5 1 171.60 209.60
##
## Step: AIC=189.33
## RFS.event ~ NEK2 + ABCD3 + MPP3 + CACNG2 + DRD4 + GJA5 + PPIA +
## CKB + HOXB5 + DLG2 + SHC3 + DUT + RPS6 + SLC22A4 + PROX1 +
## TLR1 + BID + STAT3 + FH + LDHA
##
## Df Deviance AIC
## <none> 147.34 189.34
## + TFDP2 1 145.37 189.37
## + MME 1 145.43 189.43
## + FPR1 1 145.56 189.56
## + B4GALT2 1 145.57 189.57
## - LDHA 1 149.63 189.63
## + NAP1L4 1 145.65 189.65
## + TMEM2 1 145.70 189.70
## - DRD4 1 149.71 189.71
## + CLK3 1 145.78 189.78
## - FH 1 149.97 189.97
## + TGM3 1 146.03 190.03
## + ADD2 1 146.19 190.19
## + SLC26A4 1 146.21 190.21
## + CR1 1 146.23 190.23
## - STAT3 1 150.25 190.25
## - DUT 1 150.32 190.32
## - RPS6 1 150.38 190.38
## + TGFBR2 1 146.42 190.42
## + ADD1 1 146.46 190.46
## + FBXW2 1 146.47 190.47
## + JAK3 1 146.49 190.49
## + RAB7L1 1 146.62 190.62
## + FGF6 1 146.63 190.63
## + UCP1 1 146.65 190.65
## + GATA4 1 146.68 190.68
## + RPS20 1 146.68 190.68
## + KIR2DS3 1 146.69 190.69
## + HOXC10 1 146.71 190.71
## + RPS11 1 146.73 190.73
## + CRK 1 146.79 190.79
## + CACNA1C 1 146.79 190.79
## + EWSR1 1 146.81 190.81
## + NOL4 1 146.81 190.81
## + CDS1 1 146.82 190.82
## + KLRB1 1 146.82 190.82
## + TMOD2 1 146.84 190.84
## + BNIP2 1 146.86 190.86
## + LARGE 1 146.94 190.94
## + ACADL 1 146.97 190.97
## + SRD5A2 1 146.98 190.98
## + AGL 1 146.99 190.99
## + IFNA5 1 147.00 191.00
## + ESR2 1 147.07 191.07
## + CLIC2 1 147.10 191.10
## + PDE7A 1 147.10 191.10
## + HSD3B1 1 147.11 191.11
## + HDAC6 1 147.12 191.12
## + GOT2 1 147.13 191.13
## + CAMK2B 1 147.14 191.14
## + FCER1G 1 147.14 191.14
## + HNRPDL 1 147.15 191.15
## + OAZ3 1 147.15 191.15
## + RFC5 1 147.15 191.15
## + MMD 1 147.16 191.16
## + TNFRSF9 1 147.16 191.16
## + PBX1 1 147.17 191.17
## + CHST2 1 147.19 191.19
## + ACTR3 1 147.19 191.19
## + PMAIP1 1 147.20 191.20
## + AXIN1 1 147.20 191.20
## + SPAG6 1 147.22 191.22
## + CA11 1 147.25 191.25
## + APRT 1 147.26 191.26
## + ADCY8 1 147.26 191.26
## + SLC6A14 1 147.26 191.26
## + GGA1 1 147.27 191.27
## + CDC42BPB 1 147.28 191.28
## + ACADSB 1 147.28 191.28
## + TIA1 1 147.30 191.30
## + SRI 1 147.31 191.31
## + CRYBA1 1 147.32 191.32
## + ZNF202 1 147.32 191.32
## + ATP12A 1 147.32 191.32
## + CLDN14 1 147.32 191.32
## + DOM3Z 1 147.33 191.33
## + SLC19A1 1 147.33 191.33
## + IRF3 1 147.33 191.33
## + SLC6A5 1 147.33 191.33
## + PECI 1 147.33 191.33
## + MAP7 1 147.33 191.33
## + CD209 1 147.33 191.33
## + ACYP1 1 147.33 191.33
## + MGAM 1 147.33 191.33
## + VPS35 1 147.33 191.33
## + NUP98 1 147.34 191.34
## + CYP39A1 1 147.34 191.34
## - HOXB5 1 151.57 191.57
## - SLC22A4 1 152.20 192.20
## - CKB 1 152.76 192.76
## - TLR1 1 153.09 193.09
## - BID 1 153.40 193.40
## - PROX1 1 154.47 194.47
## - DLG2 1 157.40 197.40
## - SHC3 1 158.85 198.85
## - PPIA 1 158.94 198.94
## - NEK2 1 161.97 201.97
## - MPP3 1 164.29 204.29
## - CACNG2 1 165.22 205.22
## - ABCD3 1 166.57 206.57
## - GJA5 1 167.02 207.02make ROC object
pred = predict(stepFit, newdata=tsDat, type='response')
rocObj = roc(tr.gDat$RFS.event, pred, ci=T)
cut = prop.table(table(trDat$RFS.event))[2]Cross validation
splt = rep(1:10, rep(c(20,19), c(7,3)))
pred = rep(0, nrow(trDat))
predR = rep(0, nrow(trDat))
for(i in 1:10){
trCV = trDat[splt!=i,]
tsCV = trDat[splt==i,]
f = as.formula(RFS.event ~ ER + Grade + tumor.size + node.status)
stepFit = glm(RFS.event ~ 1,family='binomial', data=trCV)
stepFit = step(stepFit, scope=f)
pred[splt==i] = predict(stepFit, newdata=tsCV, type='response')
cut = sum(trCV$RFS.event) / nrow(trCV)
predR[splt==i] = ifelse(pred[splt==i] > cut, 1, 0)
}## Start: AIC=235.81
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 211.35 215.35
## + ER 1 229.52 233.52
## <none> 233.81 235.81
## + tumor.size 1 232.41 236.41
## + node.status 1 233.81 237.81
##
## Step: AIC=215.35
## RFS.event ~ Grade
##
## Df Deviance AIC
## <none> 211.35 215.35
## + ER 1 210.98 216.98
## + tumor.size 1 211.07 217.07
## + node.status 1 211.33 217.33
## - Grade 1 233.81 235.81
## Start: AIC=237.79
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 215.27 219.27
## + ER 1 226.19 230.19
## + tumor.size 1 233.05 237.05
## <none> 235.79 237.79
## + node.status 1 235.56 239.56
##
## Step: AIC=219.27
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 211.95 217.95
## <none> 215.27 219.27
## + node.status 1 214.75 220.75
## + tumor.size 1 215.22 221.22
## - Grade 1 235.79 237.79
##
## Step: AIC=217.95
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 211.95 217.95
## - ER 1 215.27 219.27
## + node.status 1 211.41 219.41
## + tumor.size 1 211.90 219.90
## - Grade 1 226.19 230.19
## Start: AIC=237.79
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 219.44 223.44
## + ER 1 228.57 232.57
## + tumor.size 1 232.00 236.00
## <none> 235.79 237.79
## + node.status 1 235.31 239.31
##
## Step: AIC=223.44
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 217.44 223.44
## <none> 219.44 223.44
## + node.status 1 219.02 225.02
## + tumor.size 1 219.26 225.26
## - Grade 1 235.79 237.79
##
## Step: AIC=223.44
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 217.44 223.44
## - ER 1 219.44 223.44
## + node.status 1 216.87 224.87
## + tumor.size 1 217.25 225.25
## - Grade 1 228.57 232.57
## Start: AIC=239.58
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 221.80 225.80
## + ER 1 228.97 232.97
## + tumor.size 1 235.04 239.04
## <none> 237.58 239.58
## + node.status 1 237.52 241.52
##
## Step: AIC=225.8
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 218.61 224.61
## <none> 221.80 225.80
## + node.status 1 221.61 227.61
## + tumor.size 1 221.72 227.72
## - Grade 1 237.58 239.58
##
## Step: AIC=224.61
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 218.61 224.61
## - ER 1 221.80 225.80
## + node.status 1 218.35 226.35
## + tumor.size 1 218.53 226.53
## - Grade 1 228.97 232.97
## Start: AIC=240.41
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 218.60 222.60
## + ER 1 231.25 235.25
## <none> 238.41 240.41
## + tumor.size 1 237.11 241.11
## + node.status 1 238.34 242.34
##
## Step: AIC=222.6
## RFS.event ~ Grade
##
## Df Deviance AIC
## <none> 218.60 222.60
## + ER 1 216.72 222.72
## + tumor.size 1 218.40 224.40
## + node.status 1 218.57 224.57
## - Grade 1 238.41 240.41
## Start: AIC=238.71
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 218.06 222.06
## + ER 1 228.92 232.92
## + tumor.size 1 233.90 237.90
## <none> 236.71 238.71
## + node.status 1 236.70 240.70
##
## Step: AIC=222.06
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 215.62 221.62
## <none> 218.06 222.06
## + node.status 1 217.96 223.96
## + tumor.size 1 218.00 224.00
## - Grade 1 236.71 238.71
##
## Step: AIC=221.62
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 215.62 221.62
## - ER 1 218.06 222.06
## + node.status 1 215.47 223.47
## + tumor.size 1 215.53 223.53
## - Grade 1 228.92 232.92
## Start: AIC=242.6
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 223.47 227.47
## + ER 1 233.65 237.65
## <none> 240.60 242.60
## + tumor.size 1 240.04 244.04
## + node.status 1 240.59 244.59
##
## Step: AIC=227.47
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 221.42 227.42
## <none> 223.47 227.47
## + tumor.size 1 222.98 228.98
## + node.status 1 223.47 229.47
## - Grade 1 240.60 242.60
##
## Step: AIC=227.42
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 221.42 227.42
## - ER 1 223.47 227.47
## + tumor.size 1 220.93 228.93
## + node.status 1 221.41 229.41
## - Grade 1 233.65 237.65
## Start: AIC=240.59
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 220.11 224.11
## + ER 1 226.05 230.05
## <none> 238.59 240.59
## + tumor.size 1 237.52 241.52
## + node.status 1 238.44 242.44
##
## Step: AIC=224.11
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 215.54 221.54
## <none> 220.11 224.11
## + node.status 1 219.69 225.69
## + tumor.size 1 219.69 225.69
## - Grade 1 238.59 240.59
##
## Step: AIC=221.54
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 215.54 221.54
## + tumor.size 1 215.04 223.04
## + node.status 1 215.12 223.12
## - ER 1 220.11 224.11
## - Grade 1 226.05 230.05
## Start: AIC=240.59
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 221.34 225.34
## + ER 1 227.40 231.40
## + tumor.size 1 235.45 239.45
## <none> 238.59 240.59
## + node.status 1 238.32 242.32
##
## Step: AIC=225.34
## RFS.event ~ Grade
##
## Df Deviance AIC
## + ER 1 216.14 222.14
## <none> 221.34 225.34
## + node.status 1 220.98 226.98
## + tumor.size 1 221.28 227.28
## - Grade 1 238.59 240.59
##
## Step: AIC=222.14
## RFS.event ~ Grade + ER
##
## Df Deviance AIC
## <none> 216.14 222.14
## + node.status 1 215.63 223.63
## + tumor.size 1 216.05 224.05
## - ER 1 221.34 225.34
## - Grade 1 227.40 231.40
## Start: AIC=237.77
## RFS.event ~ 1
##
## Df Deviance AIC
## + Grade 1 216.81 220.81
## + ER 1 228.69 232.69
## <none> 235.77 237.77
## + tumor.size 1 234.23 238.23
## + node.status 1 235.62 239.62
##
## Step: AIC=220.81
## RFS.event ~ Grade
##
## Df Deviance AIC
## <none> 216.81 220.81
## + ER 1 215.13 221.13
## + node.status 1 216.53 222.53
## + tumor.size 1 216.71 222.71
## - Grade 1 235.77 237.77Make confusion table
confTab = table(tr.gDat$RFS.event, predR, dnn=c("RFS","predR"))Load data and the libraries
library(tidyverse)## ── Attaching packages ────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──## ✔ ggplot2 3.2.0 ✔ purrr 0.3.2
## ✔ tibble 2.1.3 ✔ dplyr 0.8.3
## ✔ tidyr 0.8.3 ✔ stringr 1.4.0
## ✔ readr 1.3.1 ✔ forcats 0.4.0## Warning: package 'tibble' was built under R version 3.5.2## Warning: package 'tidyr' was built under R version 3.5.2## Warning: package 'purrr' was built under R version 3.5.2## Warning: package 'dplyr' was built under R version 3.5.2## Warning: package 'forcats' was built under R version 3.5.2## ── Conflicts ───────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()library(caret)## Warning: package 'caret' was built under R version 3.5.2## Loading required package: lattice##
## Attaching package: 'caret'## The following object is masked from 'package:purrr':
##
## liftlibrary(glmnet)## Warning: package 'glmnet' was built under R version 3.5.2## Loading required package: Matrix## Warning: package 'Matrix' was built under R version 3.5.2##
## Attaching package: 'Matrix'## The following object is masked from 'package:tidyr':
##
## expand## Loading required package: foreach##
## Attaching package: 'foreach'## The following objects are masked from 'package:purrr':
##
## accumulate, when## Loaded glmnet 2.0-18##
## Attaching package: 'glmnet'## The following object is masked from 'package:pROC':
##
## auc# Load the data
data("Boston", package = "MASS")
# Split the data into training and test set
set.seed(123)
training.samples <- Boston$medv %>%
createDataPartition(p = 0.8, list = FALSE)
train.data <- Boston[training.samples, ]
test.data <- Boston[-training.samples, ]Build predictor
# Predictor variables
x <- model.matrix(medv~., train.data)[,-1]
# Outcome variable
y <- train.data$medvUse glmnet function
glmnet(x, y, alpha = 1, lambda = NULL)##
## Call: glmnet(x = x, y = y, alpha = 1, lambda = NULL)
##
## Df %Dev Lambda
## [1,] 0 0.00000 6.908000
## [2,] 1 0.09343 6.294000
## [3,] 2 0.18670 5.735000
## [4,] 2 0.26620 5.225000
## [5,] 2 0.33220 4.761000
## [6,] 2 0.38700 4.338000
## [7,] 2 0.43240 3.953000
## [8,] 2 0.47020 3.602000
## [9,] 2 0.50150 3.282000
## [10,] 3 0.53390 2.990000
## [11,] 3 0.56100 2.725000
## [12,] 3 0.58350 2.482000
## [13,] 3 0.60210 2.262000
## [14,] 3 0.61770 2.061000
## [15,] 3 0.63050 1.878000
## [16,] 3 0.64120 1.711000
## [17,] 3 0.65010 1.559000
## [18,] 3 0.65740 1.421000
## [19,] 3 0.66360 1.294000
## [20,] 4 0.66990 1.179000
## [21,] 4 0.67560 1.075000
## [22,] 4 0.68030 0.979100
## [23,] 4 0.68420 0.892200
## [24,] 4 0.68750 0.812900
## [25,] 5 0.69080 0.740700
## [26,] 5 0.69380 0.674900
## [27,] 6 0.69730 0.614900
## [28,] 7 0.70200 0.560300
## [29,] 7 0.70610 0.510500
## [30,] 8 0.70960 0.465200
## [31,] 8 0.71430 0.423800
## [32,] 8 0.71820 0.386200
## [33,] 8 0.72140 0.351900
## [34,] 10 0.72520 0.320600
## [35,] 11 0.72850 0.292100
## [36,] 11 0.73120 0.266200
## [37,] 11 0.73350 0.242500
## [38,] 11 0.73540 0.221000
## [39,] 11 0.73690 0.201400
## [40,] 11 0.73820 0.183500
## [41,] 12 0.73950 0.167200
## [42,] 12 0.74220 0.152300
## [43,] 12 0.74440 0.138800
## [44,] 12 0.74620 0.126500
## [45,] 12 0.74760 0.115200
## [46,] 12 0.74880 0.105000
## [47,] 12 0.74990 0.095660
## [48,] 12 0.75070 0.087160
## [49,] 12 0.75140 0.079420
## [50,] 12 0.75200 0.072370
## [51,] 12 0.75250 0.065940
## [52,] 12 0.75290 0.060080
## [53,] 12 0.75320 0.054740
## [54,] 12 0.75350 0.049880
## [55,] 12 0.75370 0.045450
## [56,] 12 0.75390 0.041410
## [57,] 12 0.75410 0.037730
## [58,] 12 0.75420 0.034380
## [59,] 12 0.75430 0.031330
## [60,] 12 0.75440 0.028540
## [61,] 12 0.75450 0.026010
## [62,] 12 0.75460 0.023700
## [63,] 12 0.75460 0.021590
## [64,] 12 0.75460 0.019670
## [65,] 12 0.75470 0.017930
## [66,] 12 0.75470 0.016330
## [67,] 12 0.75470 0.014880
## [68,] 12 0.75480 0.013560
## [69,] 12 0.75480 0.012360
## [70,] 12 0.75480 0.011260
## [71,] 12 0.75480 0.010260
## [72,] 12 0.75480 0.009346
## [73,] 12 0.75480 0.008516
## [74,] 12 0.75480 0.007760Choose lambda
# Find the best lambda using cross-validation
set.seed(123)
cv <- cv.glmnet(x, y, alpha = 0)
# Display the best lambda value
cv$lambda.min## [1] 0.6907672Fit the model
# Fit the final model on the training data
model <- glmnet(x, y, alpha = 0, lambda = cv$lambda.min)
# Display regression coefficients
coef(model)## 14 x 1 sparse Matrix of class "dgCMatrix"
## s0
## (Intercept) 29.172942853
## crim -0.073961766
## zn 0.035006472
## indus -0.055702961
## chas 2.485565613
## nox -11.449222575
## rm 3.976849313
## age -0.002944308
## dis -1.221350102
## rad 0.147920742
## tax -0.006358355
## ptratio -0.869860292
## black 0.009399874
## lstat -0.483051940Predictions in test data
# Make predictions on the test data
x.test <- model.matrix(medv ~., test.data)[,-1]
predictions <- model %>% predict(x.test) %>% as.vector()
# Model performance metrics
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)Find the lambda for cross-validation
# Find the best lambda using cross-validation
set.seed(123)
cv <- cv.glmnet(x, y, alpha = 1)
# Display the best lambda value
cv$lambda.min## [1] 0.007759554Fit the final model on the training data
# Fit the final model on the training data
model <- glmnet(x, y, alpha = 1, lambda = cv$lambda.min)
# Dsiplay regression coefficients
coef(model)## 14 x 1 sparse Matrix of class "dgCMatrix"
## s0
## (Intercept) 36.962374270
## crim -0.092549948
## zn 0.048543171
## indus -0.008321076
## chas 2.287418592
## nox -16.832483690
## rm 3.810180182
## age .
## dis -1.598716155
## rad 0.286797839
## tax -0.012456750
## ptratio -0.950997301
## black 0.009652895
## lstat -0.528739166Make predictions for the test data
# Make predictions on the test data
x.test <- model.matrix(medv ~., test.data)[,-1]
predictions <- model %>% predict(x.test) %>% as.vector()
# Model performance metrics
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)Build the model
# Build the model using the training set
set.seed(123)
model <- train(
medv ~., data = train.data, method = "glmnet",
trControl = trainControl("cv", number = 10),
tuneLength = 10
)
# Best tuning parameter
model$bestTuneCompare the coefficients
# Coefficient of the final model. You need
# to specify the best lambda
coef(model$finalModel, model$bestTune$lambda)## 14 x 1 sparse Matrix of class "dgCMatrix"
## 1
## (Intercept) 33.040831297
## crim -0.078982571
## zn 0.041358040
## indus -0.030932077
## chas 2.344430283
## nox -14.304415843
## rm 3.908625770
## age .
## dis -1.417832517
## rad 0.205637826
## tax -0.008793739
## ptratio -0.912137977
## black 0.009457469
## lstat -0.517696368Data set up and predictions
# Make predictions on the test data
x.test <- model.matrix(medv ~., test.data)[,-1]
predictions <- model %>% predict(x.test)
# Model performance metrics
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)comparing different models with caret
lambda <- 10^seq(-3, 3, length = 100)compute ridge
# Build the model
set.seed(123)
ridge <- train(
medv ~., data = train.data, method = "glmnet",
trControl = trainControl("cv", number = 10),
tuneGrid = expand.grid(alpha = 0, lambda = lambda)
)
# Model coefficients
coef(ridge$finalModel, ridge$bestTune$lambda)## 14 x 1 sparse Matrix of class "dgCMatrix"
## 1
## (Intercept) 29.121492610
## crim -0.073610742
## zn 0.035141041
## indus -0.055374540
## chas 2.482740701
## nox -11.346836878
## rm 3.972188854
## age -0.002762851
## dis -1.219482977
## rad 0.147552973
## tax -0.006384982
## ptratio -0.868638681
## black 0.009411196
## lstat -0.484146579# Make predictions
predictions <- ridge %>% predict(test.data)
# Model prediction performance
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)Compute lasso
# Build the model
set.seed(123)
lasso <- train(
medv ~., data = train.data, method = "glmnet",
trControl = trainControl("cv", number = 10),
tuneGrid = expand.grid(alpha = 1, lambda = lambda)
)## Warning in nominalTrainWorkflow(x = x, y = y, wts = weights, info =
## trainInfo, : There were missing values in resampled performance measures.# Model coefficients
coef(lasso$finalModel, lasso$bestTune$lambda)## 14 x 1 sparse Matrix of class "dgCMatrix"
## 1
## (Intercept) 35.10728348
## crim -0.08200262
## zn 0.04450716
## indus -0.01018598
## chas 2.24634985
## nox -15.67089999
## rm 3.86564430
## age .
## dis -1.50738293
## rad 0.24404459
## tax -0.01068364
## ptratio -0.93304025
## black 0.00946234
## lstat -0.53072789# Make predictions
predictions <- lasso %>% predict(test.data)
# Model prediction performance
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)Elastic net regression
# Build the model
set.seed(123)
elastic <- train(
medv ~., data = train.data, method = "glmnet",
trControl = trainControl("cv", number = 10),
tuneLength = 10
)
# Model coefficients
coef(elastic$finalModel, elastic$bestTune$lambda)## 14 x 1 sparse Matrix of class "dgCMatrix"
## 1
## (Intercept) 33.040831297
## crim -0.078982571
## zn 0.041358040
## indus -0.030932077
## chas 2.344430283
## nox -14.304415843
## rm 3.908625770
## age .
## dis -1.417832517
## rad 0.205637826
## tax -0.008793739
## ptratio -0.912137977
## black 0.009457469
## lstat -0.517696368# Make predictions
predictions <- elastic %>% predict(test.data)
# Model prediction performance
data.frame(
RMSE = RMSE(predictions, test.data$medv),
Rsquare = R2(predictions, test.data$medv)
)Comparing models
models <- list(ridge = ridge, lasso = lasso, elastic = elastic)
resamples(models) %>% summary( metric = "RMSE")##
## Call:
## summary.resamples(object = ., metric = "RMSE")
##
## Models: ridge, lasso, elastic
## Number of resamples: 10
##
## RMSE
## Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
## ridge 3.101448 3.956282 4.375956 4.729206 5.521857 7.429151 0
## lasso 3.159487 4.025593 4.387946 4.725619 5.514033 7.269198 0
## elastic 3.127576 4.001460 4.372290 4.721808 5.521681 7.323973 0