| read.HTSeqCounts {DEXSeq} | R Documentation |
This function reads the output files from the HTSeq python scripts dexseq_prepare_annotation.py and dexseq_count.py and gives back an ExonCountSet object.
read.HTSeqCounts(countfiles, design, flattenedfile=NULL)
countfiles |
A string vector containing the output files with the paths from dexseq_count.py. |
design |
A vector of factors with information corresponding to each of the countfiles or a data frame design (each column with a factor and each row with its respective sample. If strings are given, they will be converted to factors. |
flattenedfile |
An flattened annotation gtf file generated by dexseq_prepare_annotation.py. It is necessary for the visualization of the data but not required to test for alternative exon usage. |
An ExonCount object.
library(DEXSeq)
inDir = system.file("extdata", package="pasilla", mustWork=TRUE)
annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
samples = data.frame(
condition = c(rep("treated", 3), rep("untreated", 4)),
row.names = dir(system.file("extdata", package="pasilla", mustWork=TRUE),
pattern="fb.txt"),
stringsAsFactors = TRUE,
check.names = FALSE
)
annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)),
design = samples,
flattenedfile = annotationfile)