gRNA res MASTcpmdet result
Last updated: 2019-03-27
Checks: 5 1
Knit directory: cropseq/
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This summarizes results obtained from running module load R; Rscript code/gRNA_MASTcpmdet_run.R from shell.
library(Matrix)
load("data/DE_input.Rd")
source("code/summary_functions.R")
gRNAdm0 <- dm[(dim(dm)[1]-75):dim(dm)[1],]Using only cells with negative control gRNA as controls
for (gRNAfile in list.files("data/gRNA_MASTcpmdet/", "*MASTcpmdet_Neg1.Rd")){
print(gRNAfile)
gRNA <- strsplit(gRNAfile, "_MAST")[[1]][1]
gRNAlocus <- strsplit(gRNA, split = "_")[[1]][1]
load(paste0("data/gRNA_MASTcpmdet/", gRNAfile))
print(signif(head(res1,n=10),2))
plotgn <- rownames(res1[,][res1[,"fdr"] <0.2,])
if (length(plotgn)!=0){
summ_pvalues(res1$pval)
for (gn in plotgn){
gcount <- dm[gn, gRNAdm0[gRNA,] >0 & colSums(gRNAdm0[rownames(gRNAdm0) != gRNA,]) == 0]
ncount1 <- dm[gn, colnames(dm1dfagg)[dm1dfagg["neg",] >0 & nlocus==1]]
a <- rbind(cbind(gcount,1),cbind(ncount1,2))
colnames(a) <- c("count","categ")
boxplot(count ~categ, data = a, lwd = 2, main=paste(gRNA, gn, sep=":"), outcol="white")
stripchart(count ~categ, data=a, vertical = TRUE, method = "jitter", add = TRUE, pch = 21, cex=2, col = 'blue')
}
}
}[1] "BAG5_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
DCLK2 0.00011 1 0.74 0.16 1.9
ARAF 0.00012 1 -2.10 0.27 -4.1
EPHX2 0.00050 1 NaN NaN NaN
BAZ2B 0.00062 1 2.00 0.27 3.8
LARP1 0.00075 1 2.10 0.38 3.4
DPH3 0.00082 1 -1.20 0.11 -3.5
FSCN1 0.00120 1 0.99 0.27 1.9
PUM3 0.00150 1 -1.80 0.26 -3.5
CWF19L2 0.00160 1 -1.50 0.33 -2.7
HEXIM1 0.00170 1 -1.80 0.33 -3.1
[1] "BAG5_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
NDFIP2 0.00013 1 0.20 0.330 0.35
MLLT6 0.00028 1 NaN NaN NaN
BAG1 0.00037 1 -0.94 0.056 -4.00
CHCHD2 0.00056 1 -1.60 0.220 -3.50
MT2A 0.00060 1 1.60 0.290 3.10
PLD5 0.00078 1 NaN NaN NaN
SACS 0.00080 1 -0.40 0.300 -0.73
EPN2 0.00089 1 -1.70 0.300 -3.10
RP11-16E18.4 0.00110 1 NaN NaN NaN
ARFGAP1 0.00130 1 -2.00 0.290 -3.80
[1] "BAG5_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MAP2K7 0.00011 1 -1.90 0.200 -4.4
EPS8L1 0.00023 1 -2.00 0.320 -3.6
RPF1 0.00033 1 2.20 0.480 3.1
NDUFS3 0.00046 1 0.91 0.140 2.4
TSPAN6 0.00053 1 -1.40 0.092 -4.5
TMEM27 0.00062 1 NaN NaN NaN
MED4 0.00082 1 1.50 0.310 2.8
ETV5 0.00110 1 -1.10 0.190 -2.6
MTFR1L 0.00130 1 -1.20 0.130 -3.3
DHCR24 0.00150 1 1.10 0.510 1.5
[1] "BCL11B_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PVT1 0.00011 1 -0.61 0.86 -0.66
NR6A1 0.00037 1 0.84 0.37 1.40
PPM1E 0.00037 1 -2.00 0.54 -2.80
MLXIP 0.00056 1 NaN NaN NaN
RCOR3 0.00088 1 -0.56 0.68 -0.68
CTNNBL1 0.00092 1 2.40 1.10 2.30
PTPN18 0.00110 1 NaN NaN NaN
TGFB1I1 0.00130 1 -2.70 0.77 -3.10
GLE1 0.00160 1 NaN NaN NaN
GPSM2 0.00160 1 -0.27 0.66 -0.34
[1] "BCL11B_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
IGDCC3 6.6e-05 1 1.20 0.110 3.60
VOPP1 1.5e-04 1 2.20 0.360 3.70
CACYBP 1.7e-04 1 1.20 0.150 3.10
DNAJC9 2.3e-04 1 2.10 0.350 3.50
CCP110 2.7e-04 1 1.40 0.100 4.50
NT5M 2.8e-04 1 NaN NaN NaN
SNU13 3.3e-04 1 0.55 0.017 4.20
CNTNAP2 3.8e-04 1 0.15 0.410 0.23
HSCB 3.9e-04 1 -2.00 0.180 -4.80
SCML1 4.0e-04 1 2.10 0.200 4.70
[1] "BCL11B_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ZFY 3.1e-05 0.92 -2.400 0.54 -3.300
AHDC1 1.9e-04 1.00 -2.900 0.56 -3.800
CCDC151 3.4e-04 1.00 NaN NaN NaN
UFL1 4.6e-04 1.00 -0.030 0.77 -0.034
WDR13 8.4e-04 1.00 -2.300 0.16 -5.700
GOLGA7 9.4e-04 1.00 2.000 0.66 2.500
S100A4 1.0e-03 1.00 -0.023 0.35 -0.039
ARL4C 1.2e-03 1.00 -2.300 0.19 -5.200
FAAP20 1.4e-03 1.00 1.600 0.48 2.300
MYCL 1.6e-03 1.00 -0.980 0.78 -1.100
[1] "CHRNA3_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
AC084018.1 1.9e-06 0.055 -4.6 1.2 -4.1
PHAX 4.6e-04 1.000 4.4 1.3 4.0
ABHD17A 9.1e-04 1.000 -3.4 1.6 -2.7
PREPL 9.5e-04 1.000 -1.9 3.6 -1.0
ARID1B 9.7e-04 1.000 -3.2 1.2 -2.9
RP11-419C5.1 1.1e-03 1.000 NaN NaN NaN
DCLK1 1.4e-03 1.000 -2.3 3.6 -1.2
USP48 2.2e-03 1.000 NaN NaN NaN
SEC62 2.8e-03 1.000 2.8 2.4 1.8
HABP4 3.2e-03 1.000 NaN NaN NaN
[1] "CHRNA3_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PRKAR1A 0.00013 1 -0.66 0.330 -1.20
TOP3A 0.00017 1 NaN NaN NaN
ARFGAP3 0.00025 1 1.90 0.150 4.90
MAP3K1 0.00047 1 NaN NaN NaN
EDEM3 0.00048 1 -2.00 0.350 -3.30
C1orf21 0.00049 1 0.38 0.590 0.50
PSRC1 0.00050 1 2.10 0.700 2.50
NPPC 0.00120 1 0.26 0.480 0.37
IER5L 0.00120 1 -1.50 0.310 -2.70
RABL6 0.00120 1 0.42 0.056 1.80
[1] "CHRNA3_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
OXR1 0.00013 1 NaN NaN NaN
TMEM98 0.00034 1 2.8 1.30 2.4
TTC28 0.00043 1 NaN NaN NaN
RRP9 0.00046 1 -2.6 0.19 -5.8
CBWD1 0.00072 1 -2.4 0.57 -3.2
A1BG 0.00082 1 NaN NaN NaN
SREBF2 0.00082 1 -2.4 0.19 -5.7
ATP2A1 0.00095 1 NaN NaN NaN
NUP98 0.00120 1 -2.1 0.81 -2.3
NEDD4L 0.00150 1 NaN NaN NaN
[1] "DPYD_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
C3orf52 2.5e-05 0.73 NaN NaN NaN
RHNO1 8.8e-05 1.00 1.80 0.30 3.20
ICAM3 1.9e-04 1.00 NaN NaN NaN
KIAA1143 1.9e-04 1.00 -0.42 0.27 -0.81
TAF1C 3.2e-04 1.00 NaN NaN NaN
CROCC 3.3e-04 1.00 NaN NaN NaN
ALDH5A1 4.7e-04 1.00 NaN NaN NaN
NTRK2 6.3e-04 1.00 2.20 0.33 3.80
TLE4 6.8e-04 1.00 -1.90 0.21 -4.30
FASN 7.0e-04 1.00 1.30 0.29 2.50
[1] "DPYD_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MARCH6 2.3e-06 0.07 1.40 0.210 2.9
ARAF 9.2e-05 1.00 -1.80 0.170 -4.3
NLRX1 1.3e-04 1.00 NaN NaN NaN
PCM1 2.4e-04 1.00 -0.37 0.059 -1.5
FAM155A 2.5e-04 1.00 NaN NaN NaN
AKAP9 4.8e-04 1.00 -1.30 0.120 -3.8
PGGT1B 5.2e-04 1.00 -1.40 0.160 -3.5
APLP1 6.2e-04 1.00 -0.90 0.074 -3.3
ENPP1 6.4e-04 1.00 0.50 0.034 2.7
ABCD4 8.7e-04 1.00 -0.94 0.190 -2.2
[1] "DPYD_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SERINC2 6.9e-05 1 2.400 0.29 4.50
ID1 1.2e-04 1 0.470 0.46 0.70
SWSAP1 1.7e-04 1 0.072 0.23 0.15
LIX1L 4.9e-04 1 -0.820 0.45 -1.20
CCNF 5.5e-04 1 0.690 0.18 1.60
ATE1 5.8e-04 1 0.054 0.25 0.11
AFF3 6.6e-04 1 NaN NaN NaN
ITGA6 8.2e-04 1 -1.700 0.31 -3.00
AES 8.8e-04 1 -0.690 0.16 -1.70
NBPF20 9.3e-04 1 NaN NaN NaN
[1] "GALNT10_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PI4K2A 0.00019 1 -1.4 0.210 -3.20
PRKAR1A 0.00036 1 -1.1 0.077 -4.10
ID4 0.00052 1 2.1 0.400 3.30
CCDC50 0.00059 1 -1.7 0.180 -3.90
ZNF462 0.00061 1 0.2 0.240 0.42
JAG1 0.00072 1 1.3 0.310 2.40
PGLS 0.00083 1 0.6 0.160 1.50
CHST1 0.00095 1 NaN NaN NaN
CCM2 0.00100 1 1.0 0.380 1.70
ASH2L 0.00100 1 -1.8 0.220 -3.80
[1] "GALNT10_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
FZD3 0.00021 1 -0.910 0.050 -4.10
VDAC3 0.00026 1 -0.065 0.120 -0.19
ST7L 0.00028 1 -2.000 0.290 -3.80
YWHAG 0.00048 1 -1.100 0.084 -3.60
SCD5 0.00064 1 1.300 0.190 3.00
DRD4 0.00068 1 -0.660 0.100 -2.10
ZNF519 0.00110 1 0.880 0.140 2.30
UFSP1 0.00130 1 NaN NaN NaN
FBXL5 0.00140 1 1.700 0.250 3.40
C3orf52 0.00150 1 NaN NaN NaN
[1] "GALNT10_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
EML1 0.00013 1 1.500 0.098 4.90
SND1-IT1 0.00018 1 -1.200 0.130 -3.50
ZNF512 0.00029 1 -1.900 0.210 -4.10
EIF1B 0.00035 1 0.510 0.110 1.60
RGS5 0.00037 1 -0.390 0.280 -0.73
BEND3 0.00037 1 NaN NaN NaN
KCNH2 0.00061 1 NaN NaN NaN
DTNA 0.00067 1 1.000 0.130 2.90
GPATCH2 0.00073 1 -0.081 0.230 -0.17
GPD2 0.00083 1 NaN NaN NaN
[1] "KCTD13_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SLC25A39 2.2e-05 0.67 0.24 0.110 0.74
ARMC1 2.3e-04 1.00 -2.00 0.160 -5.10
TBC1D17 3.5e-04 1.00 1.00 0.110 3.10
GNG10 4.6e-04 1.00 1.00 0.092 3.40
EFHD1 6.0e-04 1.00 NaN NaN NaN
GNG5 6.3e-04 1.00 0.46 0.016 3.60
SND1-IT1 7.3e-04 1.00 -1.30 0.230 -2.80
SLC35E2B 7.9e-04 1.00 NaN NaN NaN
TUBA1C 8.7e-04 1.00 1.70 0.120 5.00
LMNA 9.3e-04 1.00 2.10 0.380 3.50
[1] "KCTD13_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
RP3-400N23.9 0.00042 1 -1.1 0.17 -2.80
AK4 0.00095 1 -1.9 0.34 -3.20
PEMT 0.00150 1 -1.3 0.16 -3.30
TCP1 0.00160 1 0.1 0.13 0.28
BACE2 0.00180 1 -1.2 0.31 -2.20
SH3GL1 0.00200 1 -1.1 0.11 -3.50
ZNF75A 0.00210 1 -1.8 0.26 -3.50
PGLS 0.00220 1 0.5 0.13 1.40
DPH3 0.00230 1 -1.4 0.12 -4.00
ZNF608 0.00240 1 1.0 0.34 1.70
[1] "KCTD13_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SPTLC1 3.6e-05 1 -2.800 0.160 -6.900
VPS33B 1.3e-04 1 -0.260 0.650 -0.320
MARCH6 2.0e-04 1 0.950 0.900 1.000
MED10 2.3e-04 1 1.300 1.000 1.300
TCF12 2.6e-04 1 0.018 1.000 0.017
GOLGB1 3.8e-04 1 -3.000 0.300 -5.600
PPIL2 3.8e-04 1 NaN NaN NaN
RPS4Y1 4.0e-04 1 0.910 0.084 3.200
EPS8L1 4.5e-04 1 -2.700 0.540 -3.700
HAUS7 4.6e-04 1 0.730 0.890 0.770
[1] "KMT2E_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PRPF4B 0.00028 1 2.700 0.82 3.00
CEP41 0.00030 1 0.063 1.10 0.06
EXOC6 0.00036 1 -3.300 0.50 -4.60
ROGDI 0.00068 1 -2.400 0.32 -4.20
USP47 0.00084 1 2.800 0.48 4.10
TNFRSF13C 0.00100 1 -1.200 0.45 -1.70
SLC52A2 0.00120 1 -1.300 0.17 -3.30
CCDC149 0.00130 1 -2.000 0.63 -2.50
EXOC4 0.00160 1 -0.290 0.86 -0.31
AEBP2 0.00190 1 -2.800 0.73 -3.20
[1] "KMT2E_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TEAD1 0.00017 1 -2.8 0.39 -4.5
MARCH6 0.00020 1 1.5 0.63 1.9
PIGH 0.00043 1 -2.0 0.16 -5.0
RMDN1 0.00061 1 -2.1 0.24 -4.3
AMOT 0.00065 1 -2.3 0.49 -3.3
PRR5 0.00082 1 NaN NaN NaN
COX10 0.00110 1 1.5 0.23 3.1
DUSP16 0.00130 1 -2.1 0.42 -3.2
REL 0.00140 1 NaN NaN NaN
SPSB4 0.00140 1 1.9 0.52 2.6
[1] "KMT2E_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PCYOX1 0.00032 1 0.95 0.44 1.4
COG5 0.00042 1 NaN NaN NaN
C11orf73 0.00053 1 1.60 0.48 2.4
ARHGAP22 0.00065 1 -1.40 0.36 -2.3
TRMT10B 0.00084 1 1.60 0.12 4.6
DUS3L 0.00086 1 -1.10 0.61 -1.4
RECQL 0.00097 1 NaN NaN NaN
C1orf56 0.00100 1 -2.10 0.50 -3.0
SNU13 0.00120 1 0.83 0.25 1.7
SLC38A10 0.00120 1 -2.50 0.41 -4.0
[1] "LINC00637_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
NEFM 1.6e-05 0.48 -2.900 0.320 -5.20
KIF18B 2.6e-04 1.00 NaN NaN NaN
FXYD7 3.7e-04 1.00 0.072 0.120 0.21
PKMYT1 5.1e-04 1.00 1.800 0.190 4.00
TAF3 6.9e-04 1.00 -0.350 0.250 -0.70
DERL1 7.5e-04 1.00 1.500 0.280 2.90
ZDHHC3 8.0e-04 1.00 0.880 0.280 1.70
SMAD1 8.1e-04 1.00 -1.800 0.230 -3.70
MYL5 8.5e-04 1.00 1.100 0.062 4.50
TOMM5 8.6e-04 1.00 0.120 0.280 0.23
[1] "LINC00637_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TMEM200C 9.2e-05 1 NaN NaN NaN
SRD5A1 3.5e-04 1 2.20 0.21 4.8
TACO1 9.4e-04 1 0.89 0.47 1.3
CASC3 9.5e-04 1 1.60 0.43 2.4
TRIO 1.0e-03 1 -1.80 0.31 -3.2
CDH8 1.0e-03 1 -1.60 0.29 -3.0
AC004540.5 1.2e-03 1 NaN NaN NaN
ZNFX1 1.2e-03 1 NaN NaN NaN
BTBD2 1.5e-03 1 1.10 0.22 2.3
USP33 1.8e-03 1 0.68 0.27 1.3
[1] "LINC00637_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
HES6 0.00016 1 0.860 0.170 2.10
RNF8 0.00030 1 2.000 0.230 4.10
RGS5 0.00031 1 -0.095 0.260 -0.18
UBE2E1 0.00079 1 1.100 0.230 2.40
NPTX2 0.00110 1 NaN NaN NaN
ACTR3 0.00110 1 -0.120 0.084 -0.41
CDC25A 0.00110 1 1.300 0.120 3.90
SKAP2 0.00120 1 1.200 0.110 3.70
MAMSTR 0.00150 1 NaN NaN NaN
CDH6 0.00160 1 -1.200 0.160 -3.00
[1] "LOC100507431_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
IARS2 4.9e-05 1 0.680 0.620 0.87
CHD1L 8.4e-05 1 1.700 0.540 2.40
LANCL2 1.2e-04 1 0.710 0.230 1.50
STARD7 1.5e-04 1 0.530 0.077 1.90
COL1A1 3.9e-04 1 -0.079 0.170 -0.19
DCLK1 4.2e-04 1 0.940 0.260 1.80
SUCLG2 4.4e-04 1 -2.200 0.140 -5.80
MED16 4.4e-04 1 0.850 0.720 1.00
ANAPC10 4.8e-04 1 NaN NaN NaN
GLT25D1 6.5e-04 1 -0.440 0.740 -0.51
[1] "LOC100507431_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
HES6 0.00023 1 1.50 0.310 2.6
LAPTM4A 0.00026 1 -1.20 0.260 -2.4
DHRS7 0.00031 1 -2.10 0.330 -3.7
EGFL7 0.00032 1 NaN NaN NaN
DNAJC19 0.00045 1 0.49 0.110 1.5
ZKSCAN5 0.00045 1 0.47 0.066 1.9
S100A11 0.00050 1 -0.62 0.140 -1.7
PEAK1 0.00055 1 -1.10 0.180 -2.6
ARAP3 0.00056 1 NaN NaN NaN
DACT1 0.00056 1 NaN NaN NaN
[1] "LOC100507431_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MPHOSPH6 0.00022 1 1.00 0.20 2.30
HUS1 0.00031 1 -1.80 0.21 -4.00
FAM234A 0.00051 1 -0.87 0.19 -2.00
DNAJC16 0.00069 1 -1.30 0.15 -3.20
RNASEH2B 0.00071 1 1.60 0.16 3.90
SMCO4 0.00100 1 -0.36 0.24 -0.73
SNX32 0.00110 1 NaN NaN NaN
DDR2 0.00120 1 NaN NaN NaN
STT3B 0.00150 1 1.60 0.26 3.10
NGDN 0.00150 1 -1.30 0.12 -3.90
[1] "LOC105376975_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
OGFR 7.7e-05 1 0.99 0.34 1.7
VCL 1.2e-04 1 1.20 0.42 1.9
MUC12 1.3e-04 1 -1.90 0.27 -3.6
PDIK1L 5.2e-04 1 -1.10 0.15 -2.7
NBPF20 5.8e-04 1 NaN NaN NaN
DHX8 5.9e-04 1 NaN NaN NaN
L3HYPDH 8.3e-04 1 0.51 0.14 1.4
CTC-479C5.12 1.0e-03 1 NaN NaN NaN
FNDC3A 1.3e-03 1 1.90 0.22 4.1
EDRF1 1.4e-03 1 NaN NaN NaN
[1] "LOC105376975_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
C3orf52 5.2e-05 1 NaN NaN NaN
EEF1G 3.7e-04 1 -1.700 0.17 -4.10
RP11-428O18.6 4.1e-04 1 NaN NaN NaN
C7orf26 5.5e-04 1 1.500 0.18 3.60
MCM5 5.8e-04 1 1.300 0.29 2.40
ADAM23 8.4e-04 1 NaN NaN NaN
UFSP1 8.5e-04 1 NaN NaN NaN
DPP6 8.6e-04 1 NaN NaN NaN
HIST1H3G 9.2e-04 1 NaN NaN NaN
PRR11 1.0e-03 1 0.084 0.27 0.16
[1] "LOC105376975_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ACBD3 0.00016 1 -2.60 1.30 -2.30
FAM46A 0.00051 1 -0.15 1.10 -0.14
KIF5C 0.00067 1 4.10 1.00 4.10
ZNF276 0.00090 1 -3.50 0.92 -3.70
POMK 0.00093 1 NaN NaN NaN
TMEM47 0.00130 1 -1.50 0.35 -2.50
DLGAP4 0.00130 1 3.60 1.30 3.20
OSBPL1A 0.00130 1 NaN NaN NaN
SPOCK1 0.00140 1 -2.30 1.80 -1.70
TRIM46 0.00140 1 -0.91 0.58 -1.20
[1] "miR137_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SIPA1L1 1.1e-05 0.14 -0.0031 0.20 -0.007
METTL10 1.3e-05 0.14 -0.2400 0.32 -0.420
SKAP2 1.4e-05 0.14 1.1000 0.13 3.000
FAM228B 9.7e-05 0.67 -1.8000 0.22 -3.800
MYO9A 1.1e-04 0.67 0.2900 0.16 0.720
THG1L 2.5e-04 1.00 -1.7000 0.22 -3.700
IGDCC3 2.7e-04 1.00 0.8100 0.21 1.700
RNASEH2A 3.1e-04 1.00 1.2000 0.20 2.700
C11orf49 5.2e-04 1.00 -1.2000 0.21 -2.700
PHYHIPL 8.9e-04 1.00 1.4000 0.28 2.600
[1] "miR137_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TRIM11 6.1e-05 1 2.00 0.21 4.3
NGDN 7.8e-05 1 -0.92 0.13 -2.5
POMK 2.2e-04 1 NaN NaN NaN
NBPF20 3.7e-04 1 NaN NaN NaN
RP11-732A21.3 4.2e-04 1 -1.60 0.24 -3.2
CPPED1 4.4e-04 1 -1.70 0.26 -3.4
RMDN3 4.5e-04 1 -1.50 0.26 -2.9
MTX2 5.5e-04 1 1.60 0.34 2.7
FBXL5 5.8e-04 1 1.10 0.35 1.8
CHEK2 6.4e-04 1 1.50 0.13 4.1
[1] "miR137_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ARAP3 3.1e-05 0.93 NaN NaN NaN
DST 1.3e-04 1.00 -2.100 0.240 -4.40
KCNF1 2.7e-04 1.00 0.310 0.031 1.80
ZNF660 4.3e-04 1.00 1.300 0.080 4.40
COL5A2 7.6e-04 1.00 0.150 0.065 0.57
CPSF4 8.1e-04 1.00 -1.600 0.160 -4.00
TRAF4 9.9e-04 1.00 -0.064 0.170 -0.16
ADAMTS6 1.0e-03 1.00 NaN NaN NaN
ARMCX6 1.1e-03 1.00 -0.870 0.240 -1.80
CMBL 1.1e-03 1.00 1.700 0.270 3.40
[1] "NAB2_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
S100A4 1.1e-06 0.033 0.33 0.089 1.1
FOSL2 5.8e-06 0.087 0.36 0.091 1.2
C3orf52 9.1e-05 0.780 NaN NaN NaN
LAMC1 1.1e-04 0.780 -1.50 0.240 -3.2
PPIL2 1.5e-04 0.910 0.97 0.180 2.3
PECR 2.0e-04 1.000 NaN NaN NaN
PUM3 2.8e-04 1.000 -1.40 0.260 -2.6
PSMF1 6.9e-04 1.000 1.50 0.240 3.1
XPO6 8.2e-04 1.000 -2.00 0.310 -3.6
WDR18 9.8e-04 1.000 1.40 0.230 3.0
[1] "NAB2_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MITD1 6.3e-05 1 1.40 0.640 1.80
IFI27L1 8.5e-05 1 -2.40 0.320 -4.20
GRAMD4 4.3e-04 1 -1.10 0.200 -2.40
LINC00340 4.4e-04 1 0.31 0.150 0.80
OAF 5.7e-04 1 0.75 0.063 3.00
VPS11 7.5e-04 1 -0.79 0.430 -1.20
ZNF260 8.2e-04 1 1.10 0.200 2.40
MAP2 1.1e-03 1 0.11 0.620 0.13
GNL3 1.2e-03 1 2.00 0.460 2.90
TMEM117 1.2e-03 1 NaN NaN NaN
[1] "NAB2_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PM20D2 1.9e-05 0.58 0.71 0.21 1.50
GLUL 5.5e-05 0.82 0.38 0.41 0.59
SLC19A1 8.2e-05 0.82 NaN NaN NaN
HAUS4 2.6e-04 1.00 0.48 0.23 1.00
PAK3 4.1e-04 1.00 -1.70 0.43 -2.50
HES6 4.8e-04 1.00 0.52 0.40 0.83
MYL5 6.4e-04 1.00 NaN NaN NaN
TP53 7.3e-04 1.00 2.20 0.44 3.30
PKN2 8.0e-04 1.00 -2.00 0.34 -3.40
CNOT1 8.0e-04 1.00 1.70 0.44 2.60
[1] "NGEF_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
APRT 2.0e-05 0.59 1.00 0.090 3.50
UFC1 9.2e-05 1.00 0.65 0.100 2.10
RP11-159D12.5 2.1e-04 1.00 NaN NaN NaN
SKP1 5.4e-04 1.00 0.73 0.031 4.10
ABCC4 5.5e-04 1.00 0.19 0.520 0.26
TTF2 6.3e-04 1.00 -1.10 1.000 -1.10
TCTEX1D2 7.4e-04 1.00 0.29 0.150 0.76
TEX10 7.9e-04 1.00 -3.00 0.360 -5.00
RPL26L1 9.4e-04 1.00 2.30 1.200 2.10
AKAP8L 9.5e-04 1.00 NaN NaN NaN
[1] "NGEF_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SKA3 0.00043 1 -3.60 2.70 -2.20
C2orf69 0.00073 1 -3.80 4.20 -1.80
CDCA2 0.00120 1 -4.00 4.80 -1.80
CDC42 0.00130 1 2.20 0.33 3.80
MSANTD2 0.00210 1 -3.60 3.70 -1.80
GCFC2 0.00420 1 -1.20 4.50 -0.57
CCNF 0.00420 1 -3.70 3.30 -2.00
NPRL3 0.00420 1 -2.90 3.40 -1.50
IMPA1 0.00530 1 -0.92 4.60 -0.43
AC004696.2 0.00540 1 1.60 0.46 2.40
[1] "PBRM1_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ACTA1 0.00037 1 NaN NaN NaN
CCNF 0.00088 1 -0.510 2.40 -0.340
SKA3 0.00100 1 -0.035 2.40 -0.022
YWHAB 0.00120 1 1.300 0.13 3.500
DUSP10 0.00140 1 NaN NaN NaN
DAAM2 0.00200 1 -1.900 1.80 -1.400
RBAK-RBAKDN 0.00210 1 -3.800 0.74 -4.500
STRN4 0.00220 1 -1.600 2.00 -1.100
PRDX4 0.00270 1 3.400 2.00 2.400
CHEK2 0.00290 1 -2.700 2.10 -1.900
[1] "PBRM1_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ZNF134 0.00024 1 -2.00 0.80 -2.20
RRP12 0.00030 1 0.66 0.39 1.10
SAT1 0.00055 1 -3.00 0.22 -6.30
AUNIP 0.00070 1 0.58 0.23 1.20
TRIM69 0.00074 1 1.70 0.38 2.70
TFPT 0.00077 1 2.80 0.32 4.90
TMEM132B 0.00100 1 -2.40 0.76 -2.80
PDCD2L 0.00110 1 NaN NaN NaN
ANKRD13D 0.00120 1 0.30 0.47 0.43
C5orf24 0.00120 1 1.90 0.65 2.40
[1] "PBRM1_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
HEBP1 3.2e-05 0.95 -3.10 0.77 -3.50
TPPP3 2.1e-04 1.00 -0.83 3.70 -0.43
HDAC2 2.4e-04 1.00 2.30 0.96 2.40
ZNF774 3.2e-04 1.00 NaN NaN NaN
RP11-84A19.2 3.3e-04 1.00 NaN NaN NaN
DPP6 3.7e-04 1.00 NaN NaN NaN
RGS5 3.7e-04 1.00 -3.30 2.70 -2.00
ARL6IP6 7.8e-04 1.00 NaN NaN NaN
CTC-338M12.4 8.0e-04 1.00 -1.20 2.50 -0.75
POLR3D 1.2e-03 1.00 NaN NaN NaN
[1] "PCDHA123_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
POMK 0.00012 1 NaN NaN NaN
C2orf49 0.00018 1 -1.90 0.2300 -4.00
GRN 0.00020 1 -0.85 0.2100 -1.80
PDLIM2 0.00076 1 -1.70 0.1800 -3.90
DST 0.00100 1 -1.90 0.2600 -3.70
NUP58 0.00110 1 1.60 0.1800 3.70
GOSR1 0.00130 1 -1.00 0.1900 -2.30
HES6 0.00130 1 -0.16 0.1200 -0.45
SRSF9 0.00140 1 0.31 0.0098 3.10
DZIP1L 0.00160 1 NaN NaN NaN
[1] "PCDHA123_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
KCTD10 9.9e-05 1 -1.90 0.190 -4.40
SKA3 4.9e-04 1 -0.74 0.210 -1.60
GRSF1 5.0e-04 1 -0.34 0.075 -1.20
PHF12 5.4e-04 1 0.93 0.060 3.80
PRCC 5.6e-04 1 1.50 0.190 3.40
RP11-159D12.5 8.0e-04 1 NaN NaN NaN
MAMSTR 8.7e-04 1 NaN NaN NaN
CDCA7 9.3e-04 1 1.60 0.160 3.90
PYGO2 9.5e-04 1 0.88 0.190 2.00
NPM3 1.1e-03 1 -0.18 0.085 -0.61
[1] "PCDHA123_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
NRDC 8.5e-05 1 1.300 0.210 2.900
BLOC1S2 1.5e-04 1 -0.410 0.080 -1.400
PCYOX1 2.9e-04 1 -0.320 0.230 -0.670
IGF2BP1 5.2e-04 1 1.300 0.160 3.300
RP11-591N1.1 1.3e-03 1 NaN NaN NaN
ZNF444 1.3e-03 1 -0.190 0.200 -0.420
CCZ1 1.5e-03 1 -0.670 0.160 -1.700
PPIL1 1.5e-03 1 -0.340 0.058 -1.400
SKA3 1.5e-03 1 0.022 0.200 0.049
PTPN11 1.6e-03 1 -1.500 0.240 -3.000
[1] "PPP1R16B_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SRPK2 0.00022 1 -1.20 0.120 -3.5
RTCA 0.00031 1 -1.60 0.120 -4.6
GEMIN4 0.00036 1 1.20 0.091 3.9
ELMO1 0.00037 1 1.40 0.094 4.5
HNRNPAB 0.00052 1 0.79 0.130 2.2
RAD54L 0.00100 1 1.50 0.130 4.2
ZNF273 0.00110 1 1.50 0.120 4.3
TFDP1 0.00140 1 1.10 0.250 2.3
CLUAP1 0.00150 1 1.60 0.170 3.9
GUCY1A3 0.00150 1 NaN NaN NaN
[1] "RERE_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TOLLIP 0.00041 1 0.085 0.310 0.15
TSC22D4 0.00049 1 1.500 0.120 4.40
RANGAP1 0.00050 1 -1.200 0.270 -2.40
MRPS2 0.00074 1 -0.260 0.057 -1.10
ECH1 0.00077 1 -0.580 0.094 -1.90
UFSP2 0.00092 1 0.670 0.320 1.20
SNX27 0.00120 1 -1.600 0.240 -3.20
FAM133B 0.00130 1 -0.960 0.072 -3.60
MAP3K11 0.00170 1 0.940 0.230 1.90
ISG20L2 0.00170 1 1.700 0.280 3.20
[1] "RERE_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
THAP6 1.5e-05 0.46 NaN NaN NaN
KDELR2 1.2e-04 1.00 0.72 0.040 3.60
HACD3 4.3e-04 1.00 0.73 0.170 1.80
SLC2A1 5.0e-04 1.00 1.20 0.260 2.40
RAD54L 5.2e-04 1.00 1.40 0.150 3.50
USMG5 8.7e-04 1.00 0.45 0.013 3.90
KIF9 1.2e-03 1.00 0.61 0.270 1.20
NUP37 1.7e-03 1.00 -1.70 0.230 -3.50
LINC00327 1.9e-03 1.00 NaN NaN NaN
CRBN 1.9e-03 1.00 0.27 0.280 0.51
[1] "RERE_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TLDC1 8.9e-05 1 0.690 0.22 1.50
GNG10 1.7e-04 1 NaN NaN NaN
HIPK2 1.8e-04 1 -2.100 0.13 -5.90
AC093323.3 2.0e-04 1 2.300 0.19 5.40
NAA16 2.3e-04 1 0.089 0.38 0.14
CSNK1G2 3.1e-04 1 -2.000 0.12 -5.50
MAFF 3.4e-04 1 NaN NaN NaN
MARK2 3.8e-04 1 2.200 0.23 4.50
NDUFA3 4.0e-04 1 2.300 0.55 3.10
LGALSL 7.9e-04 1 1.500 0.15 3.80
[1] "SETD1A_1st_exon_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
RGS5 0.00012 1 0.53 0.41 0.82
RAD51C 0.00015 1 -2.00 0.15 -5.30
PVT1 0.00022 1 0.29 0.26 0.57
HSPA4L 0.00036 1 0.63 0.40 1.00
QSER1 0.00036 1 NaN NaN NaN
KLHL8 0.00059 1 NaN NaN NaN
NPPC 0.00072 1 0.45 0.47 0.66
ATP5L2 0.00086 1 NaN NaN NaN
PRKD1 0.00100 1 -1.10 0.22 -2.30
NUMB 0.00130 1 NaN NaN NaN
[1] "SETD1A_1st_exon_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MPZL1 1.7e-05 0.36 -2.000 0.23 -4.100
STIM2 2.4e-05 0.36 NaN NaN NaN
ASRGL1 3.9e-05 0.39 2.800 0.34 4.800
C14orf80 8.2e-05 0.61 2.100 0.17 5.100
NQO1 1.8e-04 1.00 0.840 0.65 1.000
ZNF677 2.3e-04 1.00 -2.300 0.37 -3.800
SPOCK1 2.9e-04 1.00 -0.026 0.43 -0.039
KCTD10 3.1e-04 1.00 -2.300 0.41 -3.700
MMP2 4.8e-04 1.00 -1.900 0.40 -2.900
DTYMK 4.9e-04 1.00 1.000 0.12 3.000
[1] "SETD1A_1st_exon_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
UBB 0.00012 1 4.000 1.30 3.500
SEPHS2 0.00032 1 0.390 3.80 0.200
COX11 0.00081 1 NaN NaN NaN
DDX1 0.00084 1 2.800 3.90 1.400
POFUT1 0.00085 1 -3.900 0.49 -5.500
FAM213B 0.00110 1 0.098 4.00 0.049
MSTO1 0.00120 1 -3.900 0.63 -4.900
IGFBP2 0.00120 1 1.800 0.24 3.700
AC073479.1 0.00150 1 NaN NaN NaN
THNSL2 0.00160 1 -2.100 1.70 -1.600
[1] "STAT6_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
COQ9 0.00024 1 0.98 0.58 1.30
MTDH 0.00039 1 0.92 0.33 1.60
RP11-329L6.2 0.00041 1 -0.31 0.22 -0.66
TANK 0.00055 1 0.33 0.31 0.59
MBD4 0.00060 1 -1.90 0.26 -3.80
S100A10 0.00064 1 NaN NaN NaN
TOR1AIP1 0.00070 1 NaN NaN NaN
DCAF6 0.00110 1 NaN NaN NaN
TIGD1 0.00110 1 NaN NaN NaN
NDE1 0.00120 1 0.80 0.15 2.00
[1] "STAT6_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ELOVL2 0.00017 1 NaN NaN NaN
SP8 0.00026 1 -1.100 0.230 -2.40
IMPA2 0.00029 1 2.200 0.220 4.60
AHSA1 0.00041 1 -1.500 0.110 -4.50
CANX 0.00053 1 0.064 0.140 0.17
ACTC1 0.00073 1 0.430 0.099 1.40
NRCAM 0.00077 1 -1.100 0.170 -2.70
MIER3 0.00083 1 NaN NaN NaN
CISD3 0.00110 1 1.700 0.170 4.00
PTRH1 0.00120 1 1.500 0.160 3.90
[1] "STAT6_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
ITM2C 0.00016 1 2.00 0.260 3.9
TCEANC2 0.00016 1 NaN NaN NaN
MIER3 0.00023 1 0.73 0.052 3.2
STAU1 0.00040 1 1.40 0.270 2.8
CCDC152 0.00051 1 -1.10 0.130 -3.1
GFRA1 0.00052 1 0.40 0.160 1.0
DST 0.00053 1 -1.80 0.230 -3.7
NPAT 0.00053 1 0.83 0.054 3.6
RP11-389K14.3 0.00055 1 -0.72 0.073 -2.6
RILPL2 0.00097 1 1.10 0.066 4.3
[1] "TRANK1_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
SERPINI1 0.0010 1 -2.50 2.20 -1.70
INIP 0.0011 1 -3.00 0.85 -3.30
STON1 0.0012 1 -3.90 1.10 -3.80
MRPS34 0.0013 1 1.70 0.19 3.80
RSPH14 0.0015 1 -2.30 2.70 -1.40
FAM134B 0.0017 1 -3.80 1.20 -3.50
NRIP1 0.0021 1 -1.60 3.50 -0.82
METTL18 0.0021 1 -2.60 3.10 -1.50
SERINC2 0.0029 1 0.41 5.10 0.18
HSPB11 0.0029 1 NaN NaN NaN
[1] "TRANK1_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
FZD7 0.00016 1 -2.200 0.51 -3.100
LENG8 0.00024 1 1.100 0.25 2.100
RCC2 0.00035 1 1.500 0.53 2.100
SEPT8 0.00037 1 -2.500 0.39 -4.000
QRICH1 0.00081 1 -0.230 0.53 -0.320
ZNF143 0.00100 1 0.039 0.51 0.054
TMEM230 0.00110 1 1.600 0.48 2.400
ZNF763 0.00140 1 NaN NaN NaN
MTHFD1 0.00140 1 -1.600 0.35 -2.700
TSC22D4 0.00170 1 -1.900 0.38 -3.200
[1] "TRANK1_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
INPP5A 4.9e-05 0.86 NaN NaN NaN
PEAK1 8.6e-05 0.86 -0.95 0.075 -3.5
PUM3 8.7e-05 0.86 -1.20 0.210 -2.6
HIST1H4C 5.2e-04 1.00 1.60 0.500 2.3
KCTD10 6.1e-04 1.00 -1.70 0.180 -3.9
TAMM41 6.6e-04 1.00 -1.40 0.170 -3.5
DOLK 8.1e-04 1.00 -1.50 0.180 -3.6
ARRDC3 8.2e-04 1.00 0.49 0.160 1.2
CPSF4 9.4e-04 1.00 -1.50 0.150 -3.8
NAB2 1.0e-03 1.00 1.60 0.170 3.9
[1] "UBE2Q2P1_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
RHOJ 0.00019 1 NaN NaN NaN
SHPRH 0.00023 1 NaN NaN NaN
RGS5 0.00039 1 -0.46 1.00 -0.45
SERPINH1 0.00039 1 -0.89 0.51 -1.20
JUNB 0.00043 1 -2.20 0.51 -3.10
NRSN2 0.00058 1 NaN NaN NaN
HEXDC 0.00058 1 1.30 0.64 1.60
NQO1 0.00065 1 -3.40 0.39 -5.40
NUDT1 0.00087 1 0.12 0.41 0.19
FANCG 0.00088 1 NaN NaN NaN
[1] "UBE2Q2P1_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
RPS21 3.2e-05 0.85 1.20 0.061 4.9
GLO1 8.6e-05 0.85 1.80 1.800 1.3
EMG1 8.6e-05 0.85 3.00 2.800 1.8
IDH3A 2.5e-04 1.00 -3.40 0.240 -6.9
USP19 2.6e-04 1.00 -3.10 0.720 -3.7
SOX3 4.3e-04 1.00 2.50 2.600 1.6
CLPX 6.3e-04 1.00 -3.10 0.260 -6.1
SYNRG 6.8e-04 1.00 -3.20 0.230 -6.6
RIDA 8.1e-04 1.00 2.10 1.300 1.9
PABPC1 1.2e-03 1.00 0.93 0.057 3.9
[1] "UBE2Q2P1_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
MRPS12 0.00018 1 0.84 0.086 2.90
TPX2 0.00025 1 2.10 0.800 2.40
NAV1 0.00032 1 -2.90 0.420 -4.50
MDN1 0.00032 1 -0.56 0.990 -0.56
TAF1A 0.00084 1 -0.88 1.000 -0.87
GNG12 0.00120 1 NaN NaN NaN
ARFIP1 0.00140 1 NaN NaN NaN
ZNF71 0.00150 1 0.98 0.830 1.10
CBX6 0.00150 1 -2.00 0.190 -4.50
USP42 0.00170 1 1.20 0.230 2.50
[1] "VPS45_1_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
TTC17 1.1e-05 0.33 -3.30 0.28 -6.20
A2M 2.6e-05 0.38 -2.80 1.10 -2.70
NEDD9 1.2e-04 1.00 -3.20 0.49 -4.50
CHST1 3.4e-04 1.00 NaN NaN NaN
MT2A 3.6e-04 1.00 0.83 0.97 0.84
WDR55 5.3e-04 1.00 -2.70 0.46 -4.00
SF3B3 5.7e-04 1.00 0.15 1.10 0.15
LY6H 7.2e-04 1.00 -0.54 0.59 -0.71
CHTOP 7.4e-04 1.00 1.10 0.13 3.20
MAP3K11 8.0e-04 1.00 1.40 0.48 2.10
[1] "VPS45_2_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
NCAPH2 3.0e-05 0.71 -0.300 0.190 -0.68
VPS45 4.8e-05 0.71 1.600 0.160 4.10
ARAF 1.3e-04 1.00 -1.800 0.180 -4.20
POMK 2.3e-04 1.00 NaN NaN NaN
NINJ1 5.8e-04 1.00 1.500 0.200 3.30
ZNF134 1.0e-03 1.00 -1.400 0.150 -3.50
SLF2 1.1e-03 1.00 1.200 0.096 3.90
SUMO3 1.1e-03 1.00 0.680 0.050 3.00
HES6 1.2e-03 1.00 -0.038 0.100 -0.12
APLP1 1.2e-03 1.00 0.720 0.170 1.70
[1] "VPS45_3_gene_MASTcpmdet_Neg1.Rd"
pval fdr logFC varLogFC z
PCGF2 0.00013 1 NaN NaN NaN
LINC00173 0.00013 1 NaN NaN NaN
WDR26 0.00018 1 -2.9 0.93 -3.0
HMBS 0.00041 1 3.4 1.40 2.9
EIF2AK4 0.00051 1 3.5 1.10 3.3
UCK2 0.00073 1 NaN NaN NaN
CNOT1 0.00095 1 1.5 1.40 1.2
CTDSP2 0.00097 1 NaN NaN NaN
FMR1 0.00110 1 -3.1 0.74 -3.6
NADK 0.00120 1 NaN NaN NaNUsing all cells except the ones with targeted gRNA as controls
for (gRNAfile in list.files("data/gRNA_MASTcpmdet/", "*MASTcpmdet_Neg2.Rd")){
print(gRNAfile)
gRNA <- strsplit(gRNAfile, "_MAST")[[1]][1]
gRNAlocus <- strsplit(gRNA, split = "_")[[1]][1]
load(paste0("data/gRNA_MASTcpmdet/", gRNAfile))
print(signif(head(res2,n=10),2))
plotgn <- rownames(res2[,][res2[,"fdr"] <0.2,])
if (length(plotgn)!=0){
summ_pvalues(res2$pval)
for (gn in plotgn){
gcount <- dm[gn, gRNAdm0[gRNA,] >0 & colSums(gRNAdm0[rownames(gRNAdm0) != gRNA,]) == 0]
ncount2 <- dm[gn, colnames(dm1dfagg)[dm1dfagg[gRNAlocus,] == 0]]
a <- rbind(cbind(gcount,1),cbind(ncount2,2))
colnames(a) <- c("count","categ")
boxplot(count ~categ, data = a, lwd = 2, main=paste(gRNA, gn, sep=":"), outcol="white")
stripchart(count ~categ, data=a, vertical = TRUE, method = "jitter", add = TRUE, pch = 21, cex=2, col = 'blue')
}
}
}
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] gridExtra_2.3 lattice_0.20-38 Matrix_1.2-15
loaded via a namespace (and not attached):
[1] workflowr_1.2.0 Rcpp_1.0.0 digest_0.6.18 rprojroot_1.3-2
[5] gtable_0.2.0 backports_1.1.2 git2r_0.23.0 magrittr_1.5
[9] evaluate_0.12 stringi_1.3.1 fs_1.2.6 rmarkdown_1.10
[13] tools_3.5.1 stringr_1.4.0 glue_1.3.0 yaml_2.2.0
[17] compiler_3.5.1 htmltools_0.3.6 knitr_1.20