annotateCircs-methods: Load and annotate a list of circRNA candidates

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

Description

Loads a list of splice junctions detected using find_circ.py (Memczak et al. 2013; www.circbase.org), applies quality filters, calculates circular-to-linear ratios, and extends the input with genomic features

Usage

annotateCircs(se, annot.list, assembly = c("hg19", "hg38", "mm10", "rn5",
  "rn6", "dm6", "WBcel235"), fixCoordIndexing = TRUE, ...)

## S4 method for signature 'RangedSummarizedExperiment'
annotateCircs(se, annot.list,
  assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6", "WBcel235"),
  fixCoordIndexing = TRUE, ...)

Arguments

se	a SummarizedExperiment object
annot.list	list of relevant genomic features generated using loadAnnotation()
assembly	what genome assembly the input data are coming from
fixCoordIndexing	check and fix genomic coordinate indexing?
...	other arguments

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