appendIntronicCounts: Internal function appendIntronicCounts()

In lbroseus/SIRFindeR: More stable and accurate estimation of Intron Retention levels

Description

This function counts reads overlapping independent introns intervals using ['Rsubread::featureCount()']. These counts will be merged to intron intervals provided in file "curated_introns.txt".

Usage

appendIntronicCounts(bamFile, saveDir, libraryType, verbose = FALSE)

Arguments

bamFile	Path to read alignments in a bam file.
saveDir	Name for the Project Directory will be saved. The directory should contain a file "curated_introns.txt", as output by function ['curateIntrons()'].
libraryType	Read type. Either "SE" (single-end) or "PE" (paired-end)
verbose	logical indicating if verbose information for ['featureCount()'] debugging will be generated.

Value

Intron read counts in a file names "intronic_counts.txt", saved in directory saveDir.

lbroseus/SIRFindeR documentation built on Nov. 30, 2020, 11:06 a.m.