GetNumGenesExpressed: Get the total number of genes expressed per gtf file...

In njmadrid/RNAseqQuality: Provides a set of functions for summarizing the quality of RNA-seq data.

Description

Get the total number of genes expressed per gtf file (generated via Cufflinks).

Usage

GetNumGenesExpressed(gtfDFs, covThreshold = 1)

Arguments

gtfDFs	data table structure containing Cufflinks results.
covThreshold	only genes will be count that have "cov" values above this threshold. Default value is 1.0.

Value

An integer for the total number of genes expressed per gtf file (generated via Cufflinks).

Author(s)

Nathaniel J. Madrid, Jason Byars

Examples

gtffiles <- c("transcripts_sorted.gtf")
FileCons <- mclapply(gtffiles, function(FileName) file(FileName), mc.cores=8)
gtfs <- mclapply(FileCons, function(fc) import.gff(fc, format="gtf"), mc.cores=8)
for(i in length(FileCons)) { close(FileCons[[i]]) }
gtfDFs <- mclapply(gtfs, function(gtf) as.data.frame(gtf[gtf$type=="transcript"]), mc.cores=8)
names(gtfDFs) <- basename(gtffiles)
NumGenesPerFile <- GetNumGenesExpressed(gtfDFs, 1.0)

njmadrid/RNAseqQuality documentation built on May 20, 2019, 3:32 p.m.