This is the R Markdown for Supplementary Table 12, which consists of 2 parts.
source("TF_denovolOB/denovoLOBGOB.R")#GOB_LOB
library(foreach)
tf=read.table("snv_output_tf.bed",sep="\t",stringsAsFactors=F,header=T)
tf=tf[tf$result!="SILENT",]
tfbs=unique(tf$tfbs_name)
averg_diff=foreach(i=1:length(tfbs),.combine=c) %do% mean(tf$diff[tf$tfbs_name==tfbs[i]])
diff_p=foreach(i=1:length(tfbs),.combine=c) %do% wilcox.test(tf$alt_score[tf$tfbs_name==tfbs[i]],tf$ref_score[tf$tfbs_name==tfbs[i]])$p.value
diff_q=p.adjust(diff_p,method = "BH")
tf_dt=data.frame(tfbs_name=tfbs,average_diff=averg_diff,p=diff_p,adj.p=diff_q)
write.table(tf_dt,"TF_PWM_score.xls",sep="\t",row.names=F,quote=F)
head(tf_dt)## tfbs_name average_diff p adj.p
## 1 GATA2 0.4543666 5.309514e-10 3.269543e-09
## 2 MZF1_1-4 -1.8356926 1.785788e-43 5.223430e-42
## 3 BATF::JUN -2.7544040 2.621460e-09 1.460528e-08
## 4 EGR1 -3.0780290 1.323595e-22 2.212295e-21
## 5 KLF5 -5.0599525 2.630761e-64 1.538995e-62
## 6 TFAP2A -2.5515873 2.014899e-72 2.357432e-70