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1.Sample Selection.R
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1.Sample Selection.R
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##############################################Info#########################################
############# Title: Sample Selection
############# Description: This Script is Used to Select Samples from Different Studied
############# Author: Arezo Torang
############# Date: 13-Nov-2018
###########################################################################################-
rm(list = ls())
####Samples for Immune Cell Types-------------------------------------------
####(B Cell, CD4, CD8, Mono, Neu, NK, DC, M1, M2, MQ)
library(dplyr)
library(annotables)
#human genes table
gt = grch38
##Linsley: B Cell, Mono, Neu, NK, CD4, CD8 :-------------------------------
##114 Samples: 45099 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424
Linsley <- read.table("GSE60424_GEOSubmit_FC1to11_normalized_counts.txt",
header = TRUE, sep = "", dec = ".")
#Selceting samples
Main_Linsley <- data.frame(Linsley$lib311, Linsley$lib297, Linsley$lib290,
Linsley$lib228, Linsley$lib310, Linsley$lib296,
Linsley$lib289, Linsley$lib227, Linsley$lib309,
Linsley$lib295, Linsley$lib288, Linsley$lib226,
Linsley$lib314, Linsley$lib300, Linsley$lib293,
Linsley$lib231, Linsley$lib312, Linsley$lib298,
Linsley$lib291, Linsley$lib229, Linsley$lib313,
Linsley$lib299, Linsley$lib292, Linsley$lib230,
Linsley$lib232, Linsley$lib233, Linsley$lib234,
Linsley$lib235, Linsley$lib236, Linsley$lib237,
Linsley$lib238, Linsley$lib239, Linsley$lib240,
Linsley$lib241, Linsley$lib242, Linsley$lib243,
Linsley$lib244, Linsley$lib245, Linsley$lib246,
Linsley$lib247, Linsley$lib248, Linsley$lib249,
Linsley$lib250, Linsley$lib251, Linsley$lib252,
Linsley$lib253, Linsley$lib254, Linsley$lib255,
Linsley$lib256, Linsley$lib257, Linsley$lib258,
Linsley$lib260, Linsley$lib261, Linsley$lib262,
Linsley$lib263, Linsley$lib264, Linsley$lib266,
Linsley$lib267, Linsley$lib268, Linsley$lib269,
Linsley$lib270, Linsley$lib271, Linsley$lib273,
Linsley$lib274, Linsley$lib275, Linsley$lib276,
Linsley$lib277, Linsley$lib278, Linsley$lib280,
Linsley$lib281, Linsley$lib282, Linsley$lib283,
Linsley$lib284, Linsley$lib285, Linsley$lib302,
Linsley$lib303, Linsley$lib304, Linsley$lib305,
Linsley$lib306, Linsley$lib307, Linsley$lib316,
Linsley$lib317, Linsley$lib318, Linsley$lib319,
Linsley$lib320, Linsley$lib321, Linsley$lib323,
Linsley$lib324, Linsley$lib325, Linsley$lib326,
Linsley$lib327, Linsley$lib329, Linsley$lib330,
Linsley$lib331, Linsley$lib332, Linsley$lib333,
Linsley$lib334, Linsley$lib336, Linsley$lib337,
Linsley$lib338, Linsley$lib339, Linsley$lib340,
Linsley$lib342, Linsley$lib343, Linsley$lib344,
Linsley$lib345, Linsley$lib346, Linsley$lib347,
Linsley$lib349, Linsley$lib350, Linsley$lib351,
Linsley$lib352, Linsley$lib353, Linsley$lib354)
#Name Samples
colnames(Main_Linsley) = c("B1_L","B2_L","B3_L","B4_L","Mo1_L","Mo2_L",
"Mo3_L", "Mo4_L", "Ne1_L", "Ne2_L", "Ne3_L",
"Ne4_L", "Nk1_L", "Nk2_L", "Nk3_L", "Nk4_L",
"CD4_1_L", "CD4_2_L" , "CD4_3_L", "CD4_4_L",
"CD8_1_L", "CD8_2_L", "CD8_3_L" , "CD8_4_L",
"Ne5_L","Mo5_L","B5_L","CD4_5_L", "CD8_5_L",
"Ne6_L","Mo6_L","B6_L","CD4_6_L", "CD8_6_L",
"Ne7_L","Mo7_L","B7_L","CD4_7_L", "CD8_7_L",
"Nk5_L","Ne8_L", "Mo8_L", "B8_L", "CD4_8_L",
"CD8_8_L","Ne9_L","Mo9_L","B9_L", "CD4_9_L",
"CD8_9_L","Nk6_L","Ne10_L","Mo10_L","B10_L",
"CD4_10_L", "CD8_10_L", "Ne11_L" , "Mo11_L",
"B11_L" , "CD4_11_L" , "CD8_11_L" , "Nk7_L",
"Ne12_L" , "Mo12_L" , "B12_L" , "CD4_12_L",
"CD8_12_L" , "Nk8_L" , "Ne13_L" , "Mo13_L",
"B13_L" , "CD4_13_L" , "CD8_13_L" , "Nk9_L",
"Ne14_L" , "Mo14_L" , "B14_L" , "CD4_14_L",
"CD8_14_L" , "Nk10_L" , "Ne15_L" , "Mo15_L",
"B15_L", "CD4_15_L" , "CD8_15_L" , "Nk11_L",
"Ne16_L" , "Mo16_L" , "B16_L" , "CD4_16_L",
"CD8_16_L" , "Ne17_L" , "Mo17_L" , "B17_L",
"CD4_17_L", "CD8_17_L" , "Nk12_L", "Ne18_L",
"Mo18_L" , "B18_L" , "CD4_18_L", "CD8_18_L",
"Ne19_L" , "Mo19_L" , "B19_L" , "CD4_19_L",
"CD8_19_L" , "Nk13_L" , "Ne20_L" , "Mo20_L",
"B20_L" , "CD4_20_L" , "CD8_20_L" , "Nk14_L")
Main_Linsley<-cbind(Linsley[,1], Main_Linsley[ , order(colnames(Main_Linsley))])
Names<- colnames(Main_Linsley)[-1]
#Add Gene Name with Ensname
Main_Linsley_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in% Main_Linsley[,1]),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Linsley_ID)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Linsley_ID)[1],ncol=116))
for (i in 1:dim(Main_Linsley_ID)[1]) {
if( dim(Repeat_free[which(Repeat_free[,1] %in%
Main_Linsley_ID[i,1]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Linsley_ID[i,]
Main[j,] <-data.frame(Main_Linsley_ID[i,],
Main_Linsley[which(Main_Linsley[,1] %in%
Main_Linsley_ID[i,1]),2:115])
} else {print("Repetition")}
}
Main_Linsley <- Main[1:j,]
colnames(Main_Linsley) <-c("Genes","ID",Names)
write.table(Main_Linsley, file = "Linsley.txt", sep = "\t", quote = FALSE)
##Hoek: B Cell, Mono, Neu, NK, mDC, T Cell:-----------------------------
##18 Samples: 31042 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64655
Hoek <- read.table("GSE64655_Normalized_transcript_expression_in_human_immune_cells.txt",
header = TRUE, sep = "\t", dec = ".")
#Selceting samples
Main_Hoek <- data.frame(as.numeric(gsub(",", "", Hoek$X.32)),
as.numeric(gsub(",", "", Hoek$X.36)),
as.numeric(gsub(",", "", Hoek$X.8)),
as.numeric(gsub(",", "", Hoek$X.12)),
as.numeric(gsub(",", "", Hoek$X.9)),
as.numeric(gsub(",", "", Hoek$X.10)),
as.numeric(gsub(",", "", Hoek$X.11)),
as.numeric(gsub(",", "", Hoek$X.13)),
as.numeric(gsub(",", "", Hoek$X.14)),
as.numeric(gsub(",", "", Hoek$X.15)),
as.numeric(gsub(",", "", Hoek$X.16)),
as.numeric(gsub(",", "", Hoek$X.20)),
as.numeric(gsub(",", "", Hoek$X.24)),
as.numeric(gsub(",", "", Hoek$X.28)),
as.numeric(gsub(",", "", Hoek$X.48)),
as.numeric(gsub(",", "", Hoek$X.52)),
as.numeric(gsub(",", "", Hoek$X.40)),
as.numeric(gsub(",", "", Hoek$X.44)))
#Name Samples
colnames(Main_Hoek) = c("B1_H","B2_H","D1_H","D2_H","D3_H",
"D4_H","D5_H","D6_H","D7_H","D8_H",
"Mo1_H" ,"Mo2_H" ,"Ne1_H" ,"Ne2_H",
"Nk1_H","Nk2_H","T1_H","T2_H")
Main_Hoek<-cbind(Hoek[5:dim(Main_Hoek)[1],c(1,58)],
Main_Hoek[5:dim(Main_Hoek)[1], order(colnames(Main_Hoek))])
colnames(Main_Hoek)[1:2] <- c("Genes","ID")
Names<- colnames(Main_Hoek)
#Add Gene Name with Ensname
Main_Hoek_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in% Main_Hoek[,1]),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Hoek_ID)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Hoek_ID)[1],ncol=20))
for (i in 1:dim(Main_Hoek_ID)[1]) {
if( dim(Repeat_free[which(Repeat_free[,1] %in%
Main_Hoek_ID[i,1]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Hoek_ID[i,]
Main[j,] <-data.frame(Main_Hoek_ID[i,],
Main_Hoek[which(Main_Hoek[,1] %in%
Main_Hoek_ID[i,1]),3:20])
} else {print("Repetition")}
}
Main_Hoek <- Main[1:j,]
colnames(Main_Hoek) <-Names
write.table(Main_Hoek, file = "Hoek.txt", sep = "\t", quote = FALSE)
##Beyer: M1, M2:---------------------------------------------------------
##6 Samples: 18876 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36952
Beyer <- read.table("GSE36952_RPKM.txt", header = TRUE, sep = "\t", dec = ".")
#Selceting samples
Main_Beyer <- Beyer[,1:7]
#Add Gene Name with Ensname
Main_Beyer_Genes <-data.frame(gt[which(as.matrix(gt[,3]) %in%
Main_Beyer$ID),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Beyer_Genes)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Beyer_Genes)[1],ncol=8))
for (i in 1:dim(Main_Beyer_Genes)[1]) {
if( dim(Repeat_free[which(Repeat_free[,2] %in%
Main_Beyer_Genes[i,2]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Beyer_Genes[i,]
Main[j,] <-data.frame(Main_Beyer_Genes[i,],
Main_Beyer[which(Main_Beyer[,1] %in%
Main_Beyer_Genes[i,2]),2:7])
}else{print("Repetition")}
}
Main_Beyer <- Main[1:18876,]
colnames(Main_Beyer) = c("Genes","ID","M1_1_B","M1_2_B",
"M1_3_B" , "M2_1_B" , "M2_2_B",
"M2_3_B")
write.table(Main_Beyer, file = "Beyer.txt", sep = "\t", quote = FALSE)
##Zhao: MQ, NK, CD8, CD4:-----------------------------------------------
##14 Samples: 18308 Genes
####https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84697
Zhao <- read.table("GSE84697_run_RNASTAR_pipe.txt",
header = TRUE, sep = "\t", dec = ".")
#Selceting samples
Main_Zhao <- data.frame(Zhao$GENE,Zhao$s_RCC290_1,Zhao$s_RCC344hg_1,
Zhao$s_RCC351_1 , Zhao$s_RCC290_2,
Zhao$s_RCC343_2,Zhao$s_RCC344cc_1,
Zhao$s_RCC344hg_2,Zhao$s_RCC351_2,
Zhao$s_RCC343_4,Zhao$s_RCC344cc_3,
Zhao$s_RCC344hg_4,Zhao$s_RCC356_1,
Zhao$s_RCC344cc_2,Zhao$s_RCC351_4)
#Add Gene Name with Ensname
Main_Zhao_Genes <-data.frame(gt[which(as.matrix(gt[,3]) %in%
Main_Zhao$ID),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Zhao_Genes)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Zhao_Genes)[1],ncol=16))
for (i in 1:dim(Main_Zhao_Genes)[1]) {
if( dim(Repeat_free[which(Repeat_free[,2] %in%
Main_Zhao_Genes[i,2]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Zhao_Genes[i,]
Main[j,] <-data.frame(Main_Zhao_Genes[i,],
Main_Zhao[which(Main_Zhao[,1] %in%
Main_Zhao_Genes[i,2]),2:15])
} else{print("Repetition")}
}
Main_Zhao <- Main[1:18308,]
colnames(Main_Zhao) = c("Genes","ID","CD4_1_Z","CD4_2_Z",
"CD4_3_Z","CD8_1_Z","CD8_2_Z",
"CD8_3_Z","CD8_4_Z","CD8_5_Z",
"MQ1_Z" , "MQ2_Z" , "MQ3_Z",
"MQ4_Z" , "NK1_Z" , "NK2_Z")
write.table(Main_Zhao, file = "Zhao.txt", sep = "\t", quote = FALSE)
##Daniel: B Cell, CD4, CD8, NK, Mono:s------------------------------------
##20 Samples: 22978 Gene
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74246
Daniel <- read.table("GSE74246_RNAseq_All_Counts.txt", header = TRUE,
sep = "\t", dec = ".")
Main_Daniel <- data.frame(Daniel$X_TranscriptID,
Daniel[,c(41:44,29:36,25:28,37:40)])
Main_Daniel_Genes <-data.frame(gt[which(as.matrix(gt[,3]) %in%
Main_Daniel[,1]),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Daniel_Genes)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Daniel_Genes)[1],ncol=22))
for (i in 1:dim(Main_Daniel_Genes)[1]) {
if( dim(Repeat_free[which(Repeat_free[,2] %in%
Main_Daniel_Genes[i,2]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Daniel_Genes[i,]
Main[j,] <-data.frame(Main_Daniel_Genes[i,],
Main_Daniel[which(Main_Daniel[,1] %in%
Main_Daniel_Genes[i,2]),2:21])
}
else{
print("Repetition")
}
}
Main_Daniel <- Main[1:j,]
colnames(Main_Daniel) = c("Genes","ID","B1_D","B2_D","B3_D",
"B4_D" , "CD4_1_D", "CD4_2_D",
"CD4_3_D","CD4_4_D","CD8_1_D",
"CD8_2_D","CD8_3_D","CD8_4_D",
"Mo1_D","Mo2_D","Mo3_D","Mo4_D",
"Nk1_D","Nk2_D","Nk3_D","Nk4_D")
write.table(Main_Daniel, file = "Daniel.txt", sep = "\t", quote = FALSE)
##Powell: mDC, Mono:------------------------------------------------------
##6 Samples: 21436 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70106
Powell <- read.table("GSE70106_counts.txt", header = TRUE,
sep = "\t", dec = ".")
Main_Powell <-data.frame(Powell$Feature,Powell$hgnc_symbol,
Powell$SM_97.CD1c_RP_1_1_CD1c,
Powell$SM_28.CD1c_RP_1_1_CD1c,
Powell$SM_D36.COK_RP_1_1_CD1c,
Powell$SM_97.CD14.Mo_RP_1_1_CD14,
Powell$SM_28.CD14.Mo_RP_1_1_CD14,
Powell$SM_D36.14.MP_RP_1_1_CD14)
Main_Powell<-cbind(Powell[5:dim(Main_Powell)[1],c(1,58)],
Main_Powell[5:dim(Main_Powell)[1],
order(colnames(Main_Powell))])
Main_Powell_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Main_Powell[,1]),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Powell_ID)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Powell_ID)[1],ncol=8))
for (i in 1:dim(Main_Powell_ID)[1]) {
if( dim(Repeat_free[which(Repeat_free[,1] %in%
Main_Powell_ID[i,1]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Powell_ID[i,]
Main[j,] <-data.frame(Main_Powell_ID[i,],
Main_Powell[which(Main_Powell[,1] %in%
Main_Powell_ID[i,1]),3:8])
}
else{
print("Repetition")
}
}
Main_Powell <- Main[1:j,]
colnames(Main_Powell) <- c("Genes","ID","D1_P","D2_P","D3_P",
"Mo1_P","Mo2_P","Mo3_P")
write.table(Main_Powell, file = "Powell.txt",
sep = "\t", quote = FALSE)
##Xue: MQ, M1, M2:-----------------------------------------------------
##9 samples: 11806 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55536
Xue <- read.table("GSE55536_HMDM_IPS_IPSDM.norm.expr.txt",
header = TRUE, sep = "\t", dec = ".")
Main_Xue <-data.frame(Xue$gene , Xue$HMDM_M1_rep1,
Xue$HDMM_M1_rep2 , Xue$HMDM_M1_rep3,
Xue$HMDM_M2_rep1 , Xue$HMDM_M2_rep2,
Xue$HMDM_M2_rep3, Xue$HMDM_MAC_rep1,
Xue$HMDM_MAC_rep2,Xue$HMDM_MAC_rep3)
Main_Xue_Genes <-data.frame(gt[which(as.matrix(gt[,3]) %in%
Main_Xue[,1]),c(1,3)])
j=0
Repeat_free=data.frame(matrix(nrow=dim(Main_Xue_Genes)[1],ncol=2))
Main=data.frame(matrix(nrow=dim(Main_Xue_Genes)[1],ncol=11))
for (i in 1:dim(Main_Xue_Genes)[1]) {
if( dim(Repeat_free[which(Repeat_free[,2] %in%
Main_Xue_Genes[i,2]),])[1]==0){
j=j+1
Repeat_free[j,] <-Main_Xue_Genes[i,]
Main[j,] <-data.frame(Main_Xue_Genes[i,],
Main_Xue[which(Main_Xue[,1] %in%
Main_Xue_Genes[i,2]),2:10])
}
else{
print("Repetition")
}
}
Main_Xue <- Main[1:j,]
colnames(Main_Xue) = c("Genes","ID","M1_1_X","M1_2_X","M1_3_X","M2_1_X",
"M2_2_X","M2_3_X","MQ1_X","MQ2_X","MQ3_X")
write.table(Main_Xue, file = "Xue.txt", sep = "\t", quote = FALSE)
####Merging Immune Cell Samples---------------------------------------------
Total_Genes <- rbind(as.matrix(Linsley[,1]),as.matrix(Hoek[,1]),
as.matrix(Beyer[,1]) , as.matrix(Zhao[,1]),
as.matrix(Daniel[,1]),as.matrix(Powell[,1]),
as.matrix(Xue[,1]))
#make unique list of genes
Total_Genes <- data.frame(Total_Genes[!duplicated(Total_Genes)])
Main_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Total_Genes[,1]),c(1,3)])
Repeat_Free_Index<-seq_along(Main_ID[,1])[!duplicated(Main_ID[,1])]
Total_Genes<-Main_ID[Repeat_Free_Index,]
colnames(Total_Genes) <-c("Genes","ID")
Total <- merge(Total_Genes,Linsley[,-2], all = TRUE)
Total <- merge(Total,Hoek[,-2], all = TRUE)
Total <- merge(Total,Beyer[,-2], all = TRUE)
Total <- merge(Total,Zhao[,-2], all = TRUE)
Total <- merge(Total,Daniel[,-2], all = TRUE)
Total <- merge(Total,Powell[,-2], all = TRUE)
Total <- merge(Total,Xue[,-2], all = TRUE)
write.table(Total, file = "Total.txt", sep = "\t", quote = FALSE)
####Samples for T helper Cells----------------------------------------------
####(Th1, Th2, Th17, Th0, iTreg)
##Kanduri: Th1,Th2:--------------------------------------------------------
##6 Samples: 18880 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71645
Kanduri <- read.table("GSE71645_Expression_Normalized_DESeq.txt",
header = TRUE, sep = "\t", dec = ".")
Main_Kanduri<-Kanduri[,c(1,5:10)]
colnames(Main_Kanduri)[1]<-"Entrez"
library("org.Hs.eg.db")
Genes_Entrez <- as.list(org.Hs.egENSEMBL2EG)
Genes_Entrez<-data.frame(unlist(Genes_Entrez))
Genes_Entrez <- data.frame(row.names(Genes_Entrez),Genes_Entrez)
colnames(Genes_Entrez)<-c("Genes","Entrez")
Repeat_Free_Index<-seq_along(Genes_Entrez[,2])[!duplicated(Genes_Entrez[,2])]
Genes_Entrez<-Genes_Entrez[Repeat_Free_Index,]
Main_Kanduri_Entrez<-merge(Genes_Entrez,Main_Kanduri)
Main_Kanduri_Entrez<-Main_Kanduri_Entrez[,c(2,1,3:8)]
Main_Kanduri_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Main_Kanduri_Entrez[,1]),c(1,3)])
Repeat_Free_Index<-seq_along(Main_Kanduri_ID[,2])[!duplicated(Main_Kanduri_ID[,2])]
Main_Kanduri_ID<-Main_Kanduri_ID[Repeat_Free_Index,]
colnames(Main_Kanduri_ID)<-c("Genes","ID")
Main_Kanduri<-merge(Main_Kanduri_ID,Main_Kanduri_Entrez)
Main_Kanduri<-Main_Kanduri[,-3]
colnames(Main_Kanduri)<-c("Genes","ID","Th1_1_K","Th1_2_K",
"Th1_3_K", "Th2_1_K" , "Th2_2_K",
"Th2_3_K")
write.table(Main_Kanduri, file = "Kanduri.txt",
sep = "\t", quote = FALSE)
##Spurlock: Th1,Th2,Th17:---------------------------------------------------
##12 Samples: 46609 Genes
##https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66261
Spurlock <- read.table("GSE66261_read_count_table.txt",
header = TRUE, sep = "\t", dec = ".")
Main_Spurlock<-Spurlock[,c(1:3,6,9,12,4,7,10,
13,5,8,11,14)]
colnames(Main_Spurlock)[1]<-c("Genes")
Main_Spurlock_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Main_Spurlock[,1]),c(1,3)])
Repeat_Free_Index<-seq_along(Main_Spurlock_ID[,2])[!duplicated(Main_Spurlock_ID[,2])]
Main_Spurlock_ID<-Main_Spurlock_ID[Repeat_Free_Index,]
colnames(Main_Spurlock_ID)<-c("Genes","ID")
Main_Spurlock<-merge(Main_Spurlock_ID,Main_Spurlock)
Main_Spurlock<-Main_Spurlock[,-3]
colnames(Main_Spurlock)<-c("Genes","ID","Th1_1_S","Th1_2_S",
"Th1_3_S" ,"Th1_4_S" , "Th2_1_S",
"Th2_2_S" , "Th2_3_S", "Th2_4_S",
"Th17_1_S","Th17_2_S","Th17_3_S",
"Th17_4_S")
write.table(Main_Spurlock, file = "Spurlock.txt",
sep = "\t", quote = FALSE)
##Rautio: Th0,iTreg:------------------------------------------------------
##30 Samples: 35143 Genes
####https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96538
Rautio <- read.table("GSE96538_rpkm.txt", header = TRUE,
sep = "\t", dec = ".")
Main_Rautio<-data.frame(row.names(Rautio),Rautio[,c(7:11, 28:32,
49:53,17:21,
38:42,59:63)])
ENS = data.frame("data"=Main_Rautio[,1])
ENS$data = substr(ENS$data,1,15)
Main_Rautio <- data.frame(ENS,Main_Rautio[2:length(Main_Rautio)])
colnames(Main_Rautio)[1]<-c("Genes")
Main_Rautio_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Main_Rautio[,1]),c(1,3)])
Repeat_Free_Index<-seq_along(Main_Rautio_ID[,2])[!duplicated(Main_Rautio_ID[,2])]
Main_Rautio_ID<-Main_Rautio_ID[Repeat_Free_Index,]
colnames(Main_Rautio_ID)<-c("Genes","ID")
Main_Rautio<-merge(Main_Rautio_ID,Main_Rautio)
colnames(Main_Rautio)<-c("Genes","ID","Th0_1_R","Th0_2_R",
"Th0_3_R" , "Th0_4_R", "Th0_5_R",
"Th0_6_R", "Th0_7_R" , "Th0_8_R",
"Th0_9_R", "Th0_10_R","Th0_11_R",
"Th0_12_R","Th0_13_R","Th0_14_R",
"Th0_15_R","iTreg1_R","iTreg2_R",
"iTreg3_R","iTreg4_R","iTreg5_R",
"iTreg6_R","iTreg7_R","iTreg8_R",
"iTreg9_R", "iTreg10_R",
"iTreg11_R","iTreg12_R",
"iTreg13_R","iTreg14_R",
"iTreg15_R")
write.table(Main_Rautio, file = "Rautio.txt",
sep = "\t", quote = FALSE)
####Merging T helper Cell Samples-------------------------------------------
Total_Genes <- rbind(as.matrix(Kanduri[,1]),
as.matrix(Spurlock[,1]),
as.matrix(Rautio[,1]))
Total_Genes <- data.frame(Total_Genes[!duplicated(Total_Genes)])
Main_ID <-data.frame(gt[which(as.matrix(gt[,1]) %in%
Total_Genes[,1]),c(1,3)])
Repeat_Free_Index<-seq_along(Main_ID[,1])[!duplicated(Main_ID[,1])]
Total_Genes<-Main_ID[Repeat_Free_Index,]
colnames(Total_Genes) <-c("Genes","ID")
Total_Th <- merge(Total_Genes,Kanduri[,-2], all = TRUE)
Total_Th <- merge(Total_Th,Spurlock[,-2], all = TRUE)
Total_Th <- merge(Total_Th,Rautio[,-2], all = TRUE)
write.table(Total_Th, file = "Total_Th.txt",
sep = "\t", quote = FALSE)