read.HTSeqCounts {DEXSeq}R Documentation

Read counts output from HTSeq script.

Description

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.

Usage

read.HTSeqCounts(countfiles, design, flattenedfile=NULL)
     

Arguments

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.

Value

An ExonCount object.

Examples

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)),
   replicate = c(1:3, 1:4),
   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")

## Not run: 
   ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)), 
      design = samples, 
      flattenedfile = annotationfile)
       
## End(Not run)
   

[Package DEXSeq version 1.0.2 Index]