ranges2genes {CAGEr}R Documentation

ranges2genes

Description

Assign gene symbol(s) to Genomic Ranges.

Usage

ranges2genes(ranges, genes)

Arguments

ranges

Genomics Ranges object, for example extracted from a RangedSummarizedExperiment object with the rowRanges command.

genes

A GRanges object containing gene_name metadata.

Details

This private (non-exported) function is used to assign gene symbols to genomic ranges. It is run by annotateCTSS, which has to be run before CTSStoGenes.

Value

A Rle character vector of same length as the GRanges object, indicating one gene symbol or a semicolon-separated list of gene symbols for each range.

Author(s)

Charles Plessy

See Also

CTSScoordinatesGR, exampleZv9_annot

Other CAGEr annotation functions: annotateCTSS, plotAnnot, ranges2annot, ranges2names

Other CAGEr gene expression analysis functions: CTSStoGenes, GeneExpDESeq2

Examples

CAGEr:::ranges2genes(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)


[Package CAGEr version 1.24.0 Index]