psandovalv — Jan 16, 2013, 12:56 PM
# Analysis of multiple course data
# from Korbinian Strimmer (http://strimmerlab.org).
library("longitudinal")
Loading required package: corpcor
Warning: package 'corpcor' was built under R version 2.15.1
# load data set
data(tcell)
is.longitudinal(tcell.34)
[1] TRUE
attributes(tcell.34)
$dim
[1] 340 58
$dimnames
$dimnames[[1]]
[1] "0-1" "0-2" "0-3" "0-4" "0-5" "0-6" "0-7" "0-8"
[9] "0-9" "0-10" "0-11" "0-12" "0-13" "0-14" "0-15" "0-16"
[17] "0-17" "0-18" "0-19" "0-20" "0-21" "0-22" "0-23" "0-24"
[25] "0-25" "0-26" "0-27" "0-28" "0-29" "0-30" "0-31" "0-32"
[33] "0-33" "0-34" "2-1" "2-2" "2-3" "2-4" "2-5" "2-6"
[41] "2-7" "2-8" "2-9" "2-10" "2-11" "2-12" "2-13" "2-14"
[49] "2-15" "2-16" "2-17" "2-18" "2-19" "2-20" "2-21" "2-22"
[57] "2-23" "2-24" "2-25" "2-26" "2-27" "2-28" "2-29" "2-30"
[65] "2-31" "2-32" "2-33" "2-34" "4-1" "4-2" "4-3" "4-4"
[73] "4-5" "4-6" "4-7" "4-8" "4-9" "4-10" "4-11" "4-12"
[81] "4-13" "4-14" "4-15" "4-16" "4-17" "4-18" "4-19" "4-20"
[89] "4-21" "4-22" "4-23" "4-24" "4-25" "4-26" "4-27" "4-28"
[97] "4-29" "4-30" "4-31" "4-32" "4-33" "4-34" "6-1" "6-2"
[105] "6-3" "6-4" "6-5" "6-6" "6-7" "6-8" "6-9" "6-10"
[113] "6-11" "6-12" "6-13" "6-14" "6-15" "6-16" "6-17" "6-18"
[121] "6-19" "6-20" "6-21" "6-22" "6-23" "6-24" "6-25" "6-26"
[129] "6-27" "6-28" "6-29" "6-30" "6-31" "6-32" "6-33" "6-34"
[137] "8-1" "8-2" "8-3" "8-4" "8-5" "8-6" "8-7" "8-8"
[145] "8-9" "8-10" "8-11" "8-12" "8-13" "8-14" "8-15" "8-16"
[153] "8-17" "8-18" "8-19" "8-20" "8-21" "8-22" "8-23" "8-24"
[161] "8-25" "8-26" "8-27" "8-28" "8-29" "8-30" "8-31" "8-32"
[169] "8-33" "8-34" "18-1" "18-2" "18-3" "18-4" "18-5" "18-6"
[177] "18-7" "18-8" "18-9" "18-10" "18-11" "18-12" "18-13" "18-14"
[185] "18-15" "18-16" "18-17" "18-18" "18-19" "18-20" "18-21" "18-22"
[193] "18-23" "18-24" "18-25" "18-26" "18-27" "18-28" "18-29" "18-30"
[201] "18-31" "18-32" "18-33" "18-34" "24-1" "24-2" "24-3" "24-4"
[209] "24-5" "24-6" "24-7" "24-8" "24-9" "24-10" "24-11" "24-12"
[217] "24-13" "24-14" "24-15" "24-16" "24-17" "24-18" "24-19" "24-20"
[225] "24-21" "24-22" "24-23" "24-24" "24-25" "24-26" "24-27" "24-28"
[233] "24-29" "24-30" "24-31" "24-32" "24-33" "24-34" "32-1" "32-2"
[241] "32-3" "32-4" "32-5" "32-6" "32-7" "32-8" "32-9" "32-10"
[249] "32-11" "32-12" "32-13" "32-14" "32-15" "32-16" "32-17" "32-18"
[257] "32-19" "32-20" "32-21" "32-22" "32-23" "32-24" "32-25" "32-26"
[265] "32-27" "32-28" "32-29" "32-30" "32-31" "32-32" "32-33" "32-34"
[273] "48-1" "48-2" "48-3" "48-4" "48-5" "48-6" "48-7" "48-8"
[281] "48-9" "48-10" "48-11" "48-12" "48-13" "48-14" "48-15" "48-16"
[289] "48-17" "48-18" "48-19" "48-20" "48-21" "48-22" "48-23" "48-24"
[297] "48-25" "48-26" "48-27" "48-28" "48-29" "48-30" "48-31" "48-32"
[305] "48-33" "48-34" "72-1" "72-2" "72-3" "72-4" "72-5" "72-6"
[313] "72-7" "72-8" "72-9" "72-10" "72-11" "72-12" "72-13" "72-14"
[321] "72-15" "72-16" "72-17" "72-18" "72-19" "72-20" "72-21" "72-22"
[329] "72-23" "72-24" "72-25" "72-26" "72-27" "72-28" "72-29" "72-30"
[337] "72-31" "72-32" "72-33" "72-34"
$dimnames[[2]]
[1] "RB1" "CCNG1" "TRAF5" "CLU" "MAPK9" "SIVA" "CD69"
[8] "ZNFN1A1" "IL4R" "MAP2K4" "JUND" "LCK" "SCYA2" "RPS6KA1"
[15] "ITGAM" "CTNNB1" "SMN1" "CASP8" "E2F4" "PCNA" "CCNC"
[22] "PDE4B" "IL16" "APC" "ID3" "SLA" "CDK4" "EGR1"
[29] "TCF12" "MCL1" "CDC2" "SOD1" "CCNA2" "PIG3" "IRAK1"
[36] "SKIIP" "MYD88" "CASP4" "TCF8" "API2" "GATA3" "RBL2"
[43] "C3X1" "IFNAR1" "FYB" "IL2RG" "CSF2RA" "MPO" "API1"
[50] "CYP19" "CIR" "CASP7" "MAP3K8" "JUNB" "IL3RA" "NFKBIA"
[57] "LAT" "AKT1"
$class
[1] "longitudinal"
$time
[1] 0 2 4 6 8 18 24 32 48 72
$repeats
[1] 34 34 34 34 34 34 34 34 34 34
tcell.34[,1:3]
RB1 CCNG1 TRAF5
0-1 17.57 16.25 17.26
0-2 17.47 16.31 17.32
0-3 17.52 16.25 17.38
0-4 17.43 16.19 17.23
0-5 17.47 16.31 17.38
0-6 17.47 16.19 17.09
0-7 17.47 16.19 17.05
0-8 17.47 16.19 17.19
0-9 17.43 16.09 17.19
0-10 17.38 16.19 17.13
0-11 17.47 16.31 17.19
0-12 17.32 16.31 17.26
0-13 17.43 16.31 17.38
0-14 17.38 16.31 17.13
0-15 17.62 16.31 17.26
0-16 17.38 16.19 17.32
0-17 17.62 16.49 17.32
0-18 17.32 16.90 17.43
0-19 17.38 16.73 17.32
0-20 17.43 16.68 17.26
0-21 17.43 16.83 17.13
0-22 17.43 16.90 17.26
0-23 17.52 16.73 17.77
0-24 17.62 16.40 17.71
0-25 17.43 16.40 17.62
0-26 17.26 16.55 17.62
0-27 17.32 16.49 17.71
0-28 16.99 16.68 17.71
0-29 17.19 16.68 17.77
0-30 17.38 16.55 17.62
0-31 17.43 16.78 17.86
0-32 17.38 16.83 17.62
0-33 17.32 16.90 17.52
0-34 17.32 16.94 17.43
2-1 17.88 16.08 17.05
2-2 17.67 15.97 16.90
2-3 17.72 15.89 16.90
2-4 17.88 15.76 16.62
2-5 17.77 15.76 16.90
2-6 17.72 16.08 16.77
2-7 17.67 15.97 16.72
2-8 17.77 15.89 16.77
2-9 17.61 15.76 16.83
2-10 17.55 15.97 16.83
2-11 17.55 15.89 16.90
2-12 17.43 15.97 16.72
2-13 17.43 15.89 16.90
2-14 17.37 16.15 16.90
2-15 17.77 15.97 16.83
2-16 17.61 16.22 16.62
2-17 17.72 15.89 16.98
2-18 18.12 16.67 17.43
2-19 17.55 16.83 17.05
2-20 17.88 16.77 16.98
2-21 17.72 16.77 17.05
2-22 18.12 16.83 17.26
2-23 17.88 16.98 17.37
2-24 17.92 16.43 17.22
2-25 17.72 16.62 17.18
2-26 17.50 16.43 17.32
2-27 17.72 16.67 17.12
2-28 17.18 16.48 17.22
2-29 16.98 16.72 17.22
2-30 16.98 16.83 17.05
2-31 17.26 16.83 17.32
2-32 17.50 16.83 16.90
2-33 17.55 16.83 17.37
2-34 17.61 16.98 17.37
4-1 17.86 16.46 17.26
4-2 17.95 15.97 17.10
4-3 18.05 15.72 17.01
4-4 18.00 15.81 17.10
4-5 17.90 15.89 17.10
4-6 18.00 16.31 16.61
4-7 18.05 15.97 16.83
4-8 18.00 15.97 17.10
4-9 18.09 15.81 17.10
4-10 18.00 15.89 16.92
4-11 18.09 15.89 17.10
4-12 17.86 15.97 17.17
4-13 17.82 15.89 17.17
4-14 17.71 15.89 17.61
4-15 17.95 15.81 17.10
4-16 18.00 16.05 17.10
4-17 17.82 16.52 17.01
4-18 18.12 16.61 17.37
4-19 17.71 16.68 17.26
4-20 17.86 16.83 17.10
4-21 17.95 16.83 17.10
4-22 17.67 16.92 17.17
4-23 17.86 17.10 17.43
4-24 18.05 16.46 17.37
4-25 17.67 16.52 17.43
4-26 17.76 16.46 17.26
4-27 17.86 16.61 17.43
4-28 17.82 16.12 17.17
4-29 17.90 16.52 17.37
4-30 17.86 16.46 17.61
4-31 17.76 16.12 17.61
4-32 17.71 16.23 17.17
4-33 17.86 16.52 17.31
4-34 17.76 16.31 17.10
6-1 17.56 15.70 16.49
6-2 17.51 15.46 16.49
6-3 17.51 15.60 16.38
6-4 17.47 15.76 16.49
6-5 17.42 15.70 16.43
6-6 17.42 15.60 16.34
6-7 17.37 15.60 16.34
6-8 17.42 15.70 16.38
6-9 17.47 15.76 16.38
6-10 17.47 15.76 16.27
6-11 17.42 15.70 16.34
6-12 17.56 15.60 16.38
6-13 17.47 15.60 16.38
6-14 17.33 15.81 16.34
6-15 17.47 15.76 16.27
6-16 17.47 15.94 16.14
6-17 17.47 15.70 16.34
6-18 17.56 16.34 16.38
6-19 17.23 16.21 16.38
6-20 17.15 16.34 16.21
6-21 17.42 16.34 16.27
6-22 17.37 16.27 16.77
6-23 17.15 16.54 17.08
6-24 17.61 15.70 17.02
6-25 17.15 15.76 17.02
6-26 17.15 16.14 17.08
6-27 17.33 15.94 16.95
6-28 17.23 15.81 16.86
6-29 17.23 16.14 16.86
6-30 17.15 16.34 16.86
6-31 17.23 16.21 16.95
6-32 17.23 16.38 16.95
6-33 17.33 15.94 16.77
6-34 17.42 16.14 16.60
8-1 17.60 16.16 17.65
8-2 17.65 16.16 16.89
8-3 17.70 16.16 17.09
8-4 17.65 16.09 17.18
8-5 17.60 16.09 16.96
8-6 17.65 16.16 17.05
8-7 17.46 15.90 17.05
8-8 17.65 17.13 16.96
8-9 17.60 16.01 17.22
8-10 17.53 16.24 17.32
8-11 17.60 16.16 17.18
8-12 17.46 16.24 17.27
8-13 17.60 16.01 17.22
8-14 17.65 16.59 17.22
8-15 17.65 16.01 17.09
8-16 17.60 16.68 17.22
8-17 17.70 16.16 17.32
8-18 17.79 16.24 17.22
8-19 17.32 16.24 17.13
8-20 17.32 16.68 17.18
8-21 17.38 16.16 17.09
8-22 17.65 16.59 17.27
8-23 17.60 16.68 17.38
8-24 17.91 15.73 17.32
8-25 17.53 16.01 17.18
8-26 17.46 15.90 17.09
8-27 17.53 16.48 17.27
8-28 17.38 16.01 17.13
8-29 17.46 16.34 17.13
8-30 17.53 16.16 16.96
8-31 17.53 16.48 17.38
8-32 17.65 16.01 17.22
8-33 17.75 16.16 17.18
8-34 17.46 16.89 17.32
18-1 17.82 16.00 17.16
18-2 17.92 16.08 17.21
18-3 17.82 16.00 17.16
18-4 17.74 16.00 17.34
18-5 17.71 15.72 17.66
18-6 17.86 16.00 17.16
18-7 17.86 15.90 17.16
18-8 17.71 16.87 17.21
18-9 17.71 15.90 17.16
18-10 17.82 16.40 17.03
18-11 17.74 16.15 17.21
18-12 17.71 16.52 17.30
18-13 17.86 16.08 17.21
18-14 17.82 16.66 17.26
18-15 17.86 16.08 17.21
18-16 17.99 16.26 17.21
18-17 17.86 16.15 17.21
18-18 18.31 16.08 17.16
18-19 18.31 16.08 17.16
18-20 18.13 16.40 16.87
18-21 17.99 16.71 16.66
18-22 18.06 16.26 16.96
18-23 17.74 16.81 17.21
18-24 18.47 16.08 16.92
18-25 17.71 16.08 17.16
18-26 17.66 16.15 16.96
18-27 17.82 16.15 17.30
18-28 17.82 16.66 17.34
18-29 17.92 16.26 17.26
18-30 17.39 16.40 17.26
18-31 17.77 16.81 17.30
18-32 17.60 16.52 17.26
18-33 17.99 16.08 17.26
18-34 17.66 16.71 17.34
24-1 17.81 16.14 17.14
24-2 17.69 16.20 16.91
24-3 17.76 16.37 17.21
24-4 17.65 16.29 17.30
24-5 17.65 16.29 17.46
24-6 17.69 16.20 17.21
24-7 17.72 16.29 17.14
24-8 17.69 16.50 17.26
24-9 17.65 16.14 17.21
24-10 17.69 16.20 17.34
24-11 17.54 16.14 18.31
24-12 17.69 16.50 17.34
24-13 17.76 16.29 17.30
24-14 17.72 16.43 17.54
24-15 17.72 16.29 17.57
24-16 17.76 16.20 17.30
24-17 17.69 16.29 17.34
24-18 18.12 15.99 17.42
24-19 17.96 16.84 17.21
24-20 18.00 15.99 17.14
24-21 18.17 16.91 17.21
24-22 18.31 15.93 17.26
24-23 18.53 16.77 17.69
24-24 17.76 15.93 17.69
24-25 17.69 15.83 17.61
24-26 17.54 16.37 17.69
24-27 17.72 15.70 17.76
24-28 17.49 16.37 17.81
24-29 17.69 15.70 17.72
24-30 17.65 16.29 17.72
24-31 17.72 15.83 17.49
24-32 17.54 16.58 17.42
24-33 17.57 15.70 17.38
24-34 17.57 16.69 17.46
32-1 17.46 16.48 16.66
32-2 17.29 16.54 16.72
32-3 17.24 16.72 16.81
32-4 17.34 16.39 16.76
32-5 17.24 16.48 16.85
32-6 17.24 16.39 16.85
32-7 17.18 16.39 16.99
32-8 17.39 16.72 16.85
32-9 17.10 16.48 16.72
32-10 17.04 16.72 16.93
32-11 17.18 16.48 16.76
32-12 17.18 16.60 16.93
32-13 17.14 16.39 16.85
32-14 16.99 16.54 16.76
32-15 17.04 16.28 16.72
32-16 17.10 16.60 16.88
32-17 17.18 16.39 16.81
32-18 17.59 16.03 17.10
32-19 17.34 16.93 16.76
32-20 17.39 15.90 16.99
32-21 17.53 17.14 16.66
32-22 17.37 16.15 17.21
32-23 17.34 17.14 17.21
32-24 17.39 16.39 17.21
32-25 17.18 15.96 16.93
32-26 17.24 16.81 17.29
32-27 17.10 15.78 17.24
32-28 16.81 17.04 17.21
32-29 17.26 15.90 17.04
32-30 17.10 16.99 17.21
32-31 17.24 16.85 17.04
32-32 17.10 17.21 16.99
32-33 17.14 16.03 17.10
32-34 17.24 16.88 17.21
48-1 16.93 16.09 17.10
48-2 16.93 16.09 16.81
48-3 16.81 16.29 16.93
48-4 16.96 16.02 17.10
48-5 16.76 16.17 16.96
48-6 16.81 16.02 17.01
48-7 16.96 16.09 17.20
48-8 16.89 16.36 17.15
48-9 16.76 16.23 17.20
48-10 16.76 16.23 17.15
48-11 16.93 16.17 17.01
48-12 16.81 16.17 17.41
48-13 16.93 16.17 17.15
48-14 16.76 16.29 17.15
48-15 16.85 16.29 17.10
48-16 16.66 16.23 17.15
48-17 16.71 16.02 17.10
48-18 16.96 16.17 17.15
48-19 16.93 16.23 16.85
48-20 17.15 15.78 16.76
48-21 17.01 16.50 16.71
48-22 17.20 15.96 17.01
48-23 16.85 16.62 17.41
48-24 17.01 15.87 17.41
48-25 16.71 15.71 17.10
48-26 16.71 16.17 17.26
48-27 16.89 15.96 17.26
48-28 16.76 16.29 17.10
48-29 16.71 15.91 17.10
48-30 16.76 16.23 17.20
48-31 16.89 16.17 17.20
48-32 16.81 16.29 17.20
48-33 16.96 15.71 17.10
48-34 16.81 16.36 17.01
72-1 16.74 16.61 16.90
72-2 17.07 16.40 16.98
72-3 17.07 16.65 17.03
72-4 17.12 16.34 17.24
72-5 16.94 16.74 17.45
72-6 17.12 16.19 17.32
72-7 17.07 16.47 17.32
72-8 17.07 16.80 17.40
72-9 16.98 16.52 17.28
72-10 16.90 16.65 17.45
72-11 17.03 16.40 17.32
72-12 17.12 16.90 17.45
72-13 17.12 16.70 17.36
72-14 17.07 16.90 17.55
72-15 17.20 16.52 17.36
72-16 17.07 16.94 17.55
72-17 17.16 16.74 17.45
72-18 17.03 15.91 17.40
72-19 17.20 16.85 17.16
72-20 17.12 16.40 16.94
72-21 17.20 16.94 16.55
72-22 17.12 15.91 17.36
72-23 16.98 16.85 18.08
72-24 17.32 16.47 17.60
72-25 17.16 15.91 17.60
72-26 17.28 16.74 17.66
72-27 17.20 16.90 17.60
72-28 17.16 16.85 17.60
72-29 16.80 16.27 17.55
72-30 17.28 16.85 17.36
72-31 17.28 16.98 17.79
72-32 16.94 17.03 17.60
72-33 17.24 15.91 17.49
72-34 17.03 16.80 17.60
# how many samples and how many genes?
dim(tcell.34)
[1] 340 58
summary(tcell.34)
Longitudinal data:
58 variables measured at 10 different time points
Total number of measurements per variable: 340
Repeated measurements: yes
To obtain the measurement design call 'get.time.repeats()'.
# plot first nine time series
plot(tcell.34, 1:9)
#####
# an artificial example with repeated measurements, irregular sampling, and unequal spacing
m <- matrix(rnorm(200), 50, 4)
z <- as.longitudinal(m, repeats=c(10,5,5,10,20), time=c(2,8,9,15,16))
plot(z, 1:4)
###################################
## dynamical partial correlation
# load tcell data
data(tcell)
get.time.repeats(tcell.34)
$time
[1] 0 2 4 6 8 18 24 32 48 72
$repeats
[1] 34 34 34 34 34 34 34 34 34 34
# dynamical partial correlation
# (this takes into account of the unequal spacings between time points)
dynpc <- dyn.pcor(tcell.34, lambda=0)
Specified shrinkage intensity lambda (correlation matrix): 0
# static partial correlation
statpc <- pcor.shrink(tcell.34, lambda=0)
Specified shrinkage intensity lambda (correlation matrix): 0
# this is NOT the same
sum((dynpc - statpc)^2)
[1] 6.603