bootstrapJunctionCounts: Internal function bootstrapJunctionCounts()

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

Description

This function computes a bootstrap estimate of gene expression by using exon-exon junction counts. It is not intended to be used alone, but as a part of the IRratio2 estimation procedure, wrapped in function ['computeIRratio2()'].

Usage

bootstrapJunctionCounts(
  bamFile,
  saveDir,
  libraryType,
  nboot = 100,
  verbose = FALSE
)

Arguments

bamFile	Path to read alignments in a bam file.
saveDir	Working project directory.
libraryType	Type of the library of RNA-seq data. Either "SE" (single-end) or "PE" (paired-end).
nboot	Number of bootstrap sample to draw (Default: 100).
verbose	logical indicating if verbose information for ['featureCount()'] debugging will be generated.

Value

Create several files with bootstrap results

See Also

['featureCount()'], ['computeIRratio2()']

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