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Downstream of salmon run
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Downstream of salmon run
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mkdir salmon
for i in quants/*/quant.sf; do mv "$i" "salmon/$(basename -- "$(dirname -- "$i")").tsv"; done
cd salmon/
R
file_names <- dir() #where you have your files
file_names
data_frame <- do.call(cbind,lapply(file_names,read.delim, header=T))
row.names(data_frame) <- data_frame[,1]
dat <- cbind(data_frame[, c(rep(FALSE,4), TRUE)])
colnames(dat) <- file_names
All_joined_countMatrixRemaining <- dat[(-grep("^TE-",rownames(dat))),]
All_joined_countMatrixRemaining$Tosum <- (sapply(strsplit(rownames(All_joined_countMatrixRemaining),"_ENS"),"[[",1))
All_joined_countMatrixRemaining$Tosum <- gsub("\\..*", "", All_joined_countMatrixRemaining$Tosum)
library(data.table)
chalBeV1 <- data.table(All_joined_countMatrixRemaining)
chalBeV1_sum <- chalBeV1[,lapply(.SD,sum),by=Tosum, .SDcols=(colnames(chalBeV1)[-(which(colnames(chalBeV1)=="Tosum"))])]
rownames(chalBeV1_sum) <- (unlist(chalBeV1_sum[,1]))
chalBeV1_sumMatrix <- as.matrix(chalBeV1_sum[,-1])
rownames(chalBeV1_sumMatrix) <- (unlist(chalBeV1_sum[,1]))
head(chalBeV1_sumMatrix)
genes <- chalBeV1_sumMatrix
######## LTR7 family
head(chalBeV2_sumMatrix)
head(chalBe)
colnames(chalBe) <- make.names(colnames(chalBe), unique=T)
head(chalBe)
TosumV1 <- gsub("-.*","", gsub("_.*", "", (sapply(strsplit(rownames(chalBe),"TE-"),"[[",2))))
head(TosumV1)
length(TosumV1)
dim(chalbe)
dim(chalBe)
chalBe$Tosum <- TosumV1
chalBeV2 <- data.table(chalBe)
chalBeV2_sum <- chalBeV2[,lapply(.SD,mean),by=Tosum, .SDcols=(colnames(chalBeV2)[-(which(colnames(chalBeV2)=="Tosum"))])]
head(chalBeV2_sum)
rownames(chalBeV2_sum) <- (unlist(chalBeV2_sum[,1]))
chalBeV2_sumMatrix <- as.matrix(chalBeV2_sum[,-1])
head(chalBeV2_sumMatrix)
rownames(chalBeV2_sumMatrix) <- (unlist(chalBeV2_sum[,1]))
head(chalBeV2_sumMatrix)
LTR7_fam <- chalBeV2_sumMatrix
counts_fam <- (rbind(genes,LTR7_fam))
countData <- as.data.frame(counts_fam)
countData$genes <- row.names(countData)
head(countData)
countData <- countData[,c(10,1:9)]
head(countData)