count_features: Read in raw counts for genomic features

In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description

Read counts from featureCounts output into a dataframe.

Usage

count_features(inFiles, verbose = TRUE)

Arguments

inFiles	Character - List of featureCounts output files (not the ones that end in "summary" or "report")
verbose	Logical - If true, reports name of each file as it's read

Details

Output dataframe has columns corresponding to featureCounts output files, and rows corresponding to features (usually genes).

Author(s)

Emma Myers

Examples

fcs = dir(paste(projectPath, "counts/exonic_counts/", sep=""), pattern="_fcounts.txt")
fcs = fcs[ which(regexpr("summary", fcs) < 0) ]
counts_nucseq_ex = count_features(paste(projectPath, "counts/exonic_counts/",fcs,sep=""))
dim(counts_nucseq_ex)
[1] 24746     7

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.