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#!/usr/bin/env Rscript
# code from vignette, modified as needed.
# http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html
library(tximportData)
dir <- system.file("extdata", package = "tximportData")
samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("c_", samples$run)
tx2gene <- read.csv(file.path(dir, "tx2gene.gencode.v27.csv"))
library(tximport)
library(readr)
txi <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance="scaledTPM")
write.table(txi$abundance, "tximport.abundance.dat", quote=F, sep="\t")
write.table(txi$counts, "tximport.counts.dat", quote=F, sep="\t")
write.table(txi$length, "tximport.length.dat", quote=F, sep="\t")
write.table(txi$countsFromAbundance, "tximport.countsFromAbundance.dat", quote=F, sep="\t")
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