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)

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