bedTracks-methods: bedTracks

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

Description

Export circRNA information from given SummarizedExperiment object to BED6-style GRangesList. This is useful to generate genome browser tracks showing circRNA candidates per sample.

Usage

bedTracks(se, score = "circ.uniq",
  min.score = unlist(ifelse(is.null(score), list(NULL), list(1))),
  max.score = unlist(ifelse(is.null(score), list(NULL), list(1000))))

## S4 method for signature 'RangedSummarizedExperiment'
bedTracks(se, score = "circ.uniq",
  min.score = unlist(ifelse(is.null(score), list(NULL), list(1))),
  max.score = unlist(ifelse(is.null(score), list(NULL), list(1000))))

Arguments

se	SummarizedExperiment object with circRNA information
score	character vector (only first element will be used) naming the assay to use as BED score (NULL to omit BED score and use '.' as a placeholder instead)
min.score	numeric vector (only first element will be used) with minimal score a circRNA must have to be included in the BED output for a given sample (NULL to include all circRNAs for all samples, even if they were not detected in that sample)
max.score	numeric vector (only first element will be used) with maximal score to be used in BED output (higher score will be truncated) (NULL to keep scores unlimited,

Value

returns a GRangesList object with BED6 circRNA data per sample

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