getcounts<-function(prefixlength=10,colss="Nss"){
if(!require("dplyr")) BiocManager::install("dplyr",update = F,ask = F)
if(!require("stringr")) BiocManager::install("stringr",update = F,ask = F)
library(dplyr)
library(stringr)
fall <- dir(pattern = "*tab")
fall1<-fall[1]
str <- str_sub(fall1,start = 1, end = prefixlength)
df.read <- read.table(fall1)
if (colss=='dUTP'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V4)
}
if (colss=='NdUTP'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V3)
}
if (colss=='Nss'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V2)
}
colnames(df.use)<-c('V1',str)
data.out<-df.use[1:4,]
for (fnow in fall) {
str <- str_sub(fnow, start = 1, end = prefixlength)
df.read <- read.table(fnow)
if (colss=='dUTP'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V4)
}
if (colss=='NdUTP'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V3)
}
if (colss=='Nss'){
df.use <- data.frame(v1 = df.read$V1, v4 = df.read$V2)
}
colnames(df.use)<-c('V1',str)
data.out <- full_join(data.out, df.use,by="V1")
}
data.out1<-data.out[-(1:4),-2]
colnames(data.out1)[2]<-str_sub(dir(pattern = "*tab")[1], start = 1, end = prefixlength)
rawcounts=data.frame(data.out1[,-1],row.names = data.out1[,1])
write.csv(rawcounts, file = 'rawcounts.csv')
return(rawcounts)
}
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