prepareBins: prepareBins

In ETHZ-INS/diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

prepareBins

Description

prepareBins

Usage

prepareBins(
  g,
  APA = NULL,
  onlyMainChr = TRUE,
  removeAntisense = TRUE,
  chrStyle = NULL,
  maxUTRbinSize = 15000,
  codingOnly = FALSE,
  genewise = FALSE,
  stranded = FALSE,
  verbose = TRUE
)

Arguments

g	A GRanges (or path to RDS file containing a GRanges) or path to a gtf file or EnsDb object containing the gene annotation.
APA	A GRanges (or path to a GRanges in RDS format) or bed file containing the alternative poly-A site database
onlyMainChr	Logical; whether to keep only main chromosomes
removeAntisense	Logical; whether to remove antisense APA sites
chrStyle	Chromosome notation to convert to (default no conversion)
maxUTRbinSize	Max width of new alternative UTR bins
codingOnly	Logical, whether to keep only coding transcripts
genewise	Logical, whether annotation should be flattened genewise
stranded	Logical, whether to perform disjoin in a stranded fashion.
verbose	Logical, whether to print run information

Details

See the vignette for more details.

Value

A 'GRanges' object.

Author(s)

Stefan Greber

Examples

data(example_gene_annotation)
bins <- prepareBins(example_gene_annotation)

ETHZ-INS/diffUTR documentation built on March 18, 2023, 8:54 a.m.