writeBedTracks-methods: writeBedTracks

In BIMSBbioinfo/ciRcus: Annotation, analysis and visualization of circRNA data

Description

Write circRNA information from given BED6-style GRangesList (or SummarizedExperiment object) to BED files (one per sample). These can be loaded as genome browser tracks showing circRNA candidates.

Usage

writeBedTracks(circs, ...)

## S4 method for signature 'GRangesList'
writeBedTracks(circs, out.prefix = "ciRcus_",
  out.suffix = ".bed", seqlevels.style = "UCSC", sort.bed = TRUE)

## S4 method for signature 'RangedSummarizedExperiment'
writeBedTracks(circs, ...)

Arguments

circs	GRangesList or SummarizedExperiment object with circRNA information
...	named arguments defined above to be passed on from {codeSummarizedExperiment-method to GRangesList-method
out.prefix	character vector (only first element will be used) specifying the prefix to use for output files (before the sample name)
out.suffix	character vector (only first element will be used) specifying the suffix to use for output files (after the sample name)
seqlevels.style	character vector (only first element will be used) specifying the seqlevels style to use for the output BED files
sort.bed	logical vector (only first element will be used) specifying whether or not to sort the BED output (by genomic coordinates)

Value

None

BIMSBbioinfo/ciRcus documentation built on May 5, 2019, 10:25 a.m.