readBSJdata: Read the chimeric data of a circSample or circExperiment.

In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

Description

The function takes a circSample or circExperiment object and reads the chimeric data for samples described in these objects.

Usage

readBSJdata(
  object,
  chromosomes = c(1:22, "X", "Y"),
  cores = 1L,
  maxGenomicDist = 1e+05,
  onlySpanning = TRUE,
  removeBadPairs = T,
  ...
)

Arguments

object	circSample or circExperiment object
chromosomes	A vector of (valid) chromosome names that is used to restrict the chimeric read data
cores	Only supported on unix! Number of cores used for parallel processing for circExperiment objets.
maxGenomicDist	Maximal allowed size between donor and acceptor (defaults to 100.000 nt).
onlySpanning	Return only BSJ spanning or all (spanning and encompassing) reads.

Value

Same as input object, but populated slot for bsj data.

Examples

#readBSJdata(testExperiment)

KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.