## [1] 142 25106
##
## concordant discordant_A discordant_B intermidiate
## 47 22 40 33
1. Bimodality Test
1.1 mclust Result
## [1] 0
1.2 GmixR Result (equal variance)
GmixR Significant Genes (equal variance)
## [1] 1148
## [1] "CTAG2" "HERC6" "HLA.DRB5" "KRT15" "LOC643719" "MX1"
## [7] "MX2" "OASL" "ACTA1" "CEACAM6" "DCD" "EPSTI1"
## [13] "FBN2" "FIT1" "GLYCTK" "GSTM1"
Density Plot for GmixR (equal variance)
Plot the GmixR model for top genes (equal variance)
1.3 GmixR Results (unequal variance)
GmixR Significant Genes (unequal variance)
## [1] 1056
## [1] "ACTA1" "ATP6V1B1" "CD300LB" "CEACAM6"
## [5] "DCD" "KRT14" "MUCL1" "MX1"
## [9] "SCGB2A2" "UNQ830" "ARG2" "C19orf48"
## [13] "MGC23985" "CD300C" "COL17A1" "CRTAC1"
## [17] "CYorf16" "DES" "DKFZP686E2158" "FLJ35934"
## [21] "FRZB" "GAGE12G" "GAGE4" "GAGE5"
Density Plot for GmixR (unequal variance)
Plot the GmixR model for top genes (unequal variance)
1.4 LNmixR Result
## [1] 3710
## [1] "MTERF" "ACTRT1" "ARHGAP23" "BLOC1S1" "C14orf11" "C14orf73"
## [7] "C1orf216" "C20orf74" "C22orf9" "CCDC142" "CDX2" "CLPTM1L"
## [13] "FANCC" "GDNF" "GYS1" "HRC" "IFNA6" "IMPAD1"
## [19] "INE1" "KPNA5" "LEMD1" "LOC283755" "LOC390231" "LOC401284"
Density Plot for LNmixR
Plot the LNmixR model for top genes
Correlate component membership (com_1 or comp_2 from LNmixR) with
cluster membership (4 clusters)
##
## Gene: C16orf50
##
## Comp_1 Comp_2 Sum
## concordant 39 8 47
## discordant_A 15 7 22
## discordant_B 15 25 40
## intermidiate 22 11 33
## Sum 91 51 142
## Chi-square test p-value: 0.0001842306
##
## Gene: RGS12
##
## Comp_1 Comp_2 Sum
## concordant 7 40 47
## discordant_A 14 8 22
## discordant_B 18 22 40
## intermidiate 9 24 33
## Sum 48 94 142
## Chi-square test p-value: 0.000256873
##
## Gene: TSEN2
##
## Comp_1 Comp_2 Sum
## concordant 11 36 47
## discordant_A 6 16 22
## discordant_B 1 39 40
## intermidiate 0 33 33
## Sum 18 124 142
## Chi-square test p-value: 0.0005184048
##
## Gene: ZNF222
##
## Comp_1 Comp_2 Sum
## concordant 25 22 47
## discordant_A 9 13 22
## discordant_B 28 12 40
## intermidiate 8 25 33
## Sum 70 72 142
## Chi-square test p-value: 0.001106822
##
## Gene: LOC643791
##
## Comp_1 Comp_2 Sum
## concordant 18 29 47
## discordant_A 18 4 22
## discordant_B 17 23 40
## intermidiate 10 23 33
## Sum 63 79 142
## Chi-square test p-value: 0.001186623
##
## Gene: LOC648796
##
## Comp_1 Comp_2 Sum
## concordant 27 20 47
## discordant_A 7 15 22
## discordant_B 21 19 40
## intermidiate 6 27 33
## Sum 61 81 142
## Chi-square test p-value: 0.001909661
##
## Gene: OSM
##
## Comp_1 Comp_2 Sum
## concordant 37 10 47
## discordant_A 18 4 22
## discordant_B 24 16 40
## intermidiate 32 1 33
## Sum 111 31 142
## Chi-square test p-value: 0.002040254
##
## Gene: MAP3K14
##
## Comp_1 Comp_2 Sum
## concordant 4 43 47
## discordant_A 8 14 22
## discordant_B 5 35 40
## intermidiate 1 32 33
## Sum 18 124 142
## Chi-square test p-value: 0.002128074
##
## Gene: LOC642974
##
## Comp_1 Comp_2 Sum
## concordant 15 32 47
## discordant_A 6 16 22
## discordant_B 25 15 40
## intermidiate 8 25 33
## Sum 54 88 142
## Chi-square test p-value: 0.002140473
##
## Gene: FHOD1
##
## Comp_1 Comp_2 Sum
## concordant 27 20 47
## discordant_A 8 14 22
## discordant_B 7 33 40
## intermidiate 13 20 33
## Sum 55 87 142
## Chi-square test p-value: 0.002199024
##
## Gene: PRKCSH
##
## Comp_1 Comp_2 Sum
## concordant 34 13 47
## discordant_A 6 16 22
## discordant_B 26 14 40
## intermidiate 16 17 33
## Sum 82 60 142
## Chi-square test p-value: 0.002299695
##
## Gene: TWIST1
##
## Comp_1 Comp_2 Sum
## concordant 36 11 47
## discordant_A 13 9 22
## discordant_B 18 22 40
## intermidiate 27 6 33
## Sum 94 48 142
## Chi-square test p-value: 0.002410177
##
## Gene: ATF4
##
## Comp_1 Comp_2 Sum
## concordant 12 35 47
## discordant_A 15 7 22
## discordant_B 12 28 40
## intermidiate 9 24 33
## Sum 48 94 142
## Chi-square test p-value: 0.00298166
##
## Gene: ELOVL7
##
## Comp_1 Comp_2 Sum
## concordant 25 22 47
## discordant_A 2 20 22
## discordant_B 12 28 40
## intermidiate 14 19 33
## Sum 53 89 142
## Chi-square test p-value: 0.003132618
##
## Gene: CDC45L
##
## Comp_1 Comp_2 Sum
## concordant 42 5 47
## discordant_A 15 7 22
## discordant_B 32 8 40
## intermidiate 18 15 33
## Sum 107 35 142
## Chi-square test p-value: 0.003291899
##
## Gene: FIGN
##
## Comp_1 Comp_2 Sum
## concordant 1 46 47
## discordant_A 6 16 22
## discordant_B 6 34 40
## intermidiate 1 32 33
## Sum 14 128 142
## Chi-square test p-value: 0.003521671
## [1] "The number of LNmixR genes which COTWIN_Clusters strongly associated with Components are: 197"
LNmixR Top Genes which COTWIN_Clusters are strongly associated with
Components
1.5 ACR Result
## [1] 24
1.6 CH Result
## [1] 32
1.8 FM Result
## [1] 258
1.10 mt Result
## [1] 1
1.11 SI Result
## [1] 0
## [1] 49
Bimodality Summary Using Euler Diagram
DD (Differentially Dispersed) Genes
DE (Differentially Expressed) Genes
Test Delta = 0 overall: These genes are different on average between
co-twins
## [1] "ABCC3" "DMRT2" "ITIH5" "SLIT3" "GLB1" "C14orf151"
## [7] "STOX1" "GLUL" "ITGB5" "SLC16A7"
DE Genes vs. DD Genes
