source("https://bioconductor.org/biocLite.R")
biocLite("ballgown")
library(ballgown)
#X is the file which contains the expression level (FPKM) of genes in each sample, which is generated by stringTie.
bg=ballgown(dataDir="X", samplePattern='tj_', meas='all')
transcript_fpkm = texpr(bg, 'FPKM')
row.names(transcript_fpkm) = transcriptNames(bg)
bg=ballgown(dataDir="X", samplePattern='tj_', meas='all')
pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=4))
stat_results = stattest(bg, feature='gene', meas='FPKM', getFC=TRUE, covariate='group')
write.csv(stat_results, 'gene_difexp.csv', row.names=F,quote=F)