prepDrseqAnno: Prepare DrSeq annotation files

In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description

To use the useMetaFeatures functionality of Rsubread::featureCounts, we need the GTF input. This function helps to produce the two annotation files ("event" and "exon") needed by drseqCount.

Usage

prepDrseqAnno(
  anno_event,
  anno.prefix = "annotation.drseq",
  anno.format = "gff2",
  remove.overlap.exon = FALSE,
  cores = max(1, detectCores() - 2),
  verbose = TRUE
)

Arguments

anno_event	a surf object
anno.prefix	character, prefix of exon/event annotation files for saving. These files are needed by Rsubread::featureCounts.
anno.format	character, e.g. "gtf", as accepted by rtracklayer::export.
remove.overlap.exon	logical, remove overlapping exons across genes (default to FALSE).
cores	integer, number of available workers, sent to nthreads of Rsubread::featureCounts.
verbose	logical, whether (TRUE) to echo progress.

Value

NULL, the function is a procedure and only output/export results to file system, except for messages and warnings.

fchen365/surf documentation built on June 18, 2021, 12:02 p.m.