ranges2annot {CAGEr}R Documentation

hierarchical annotation of CTSSes

Description

Assigns region types such as promoter, exon or unknown to CTSSes.

Usage

ranges2annot(ranges, annot)

Arguments

ranges

The CTSS (GRanges) object, for example extracted from a RangedSummarizedExperiment object with the rowRanges command.

annot

A GRanges from which promoter positions will be inferred. Typically GENCODE. If the type metadata is present, it should contain ‘gene’, ‘exon’ and ‘transcript’ among its values. Otherwise, all entries are considered transcripts. If the transcript_type metadata is available, the entries may be not primary products (for instance ‘snoRNA’) are discarded.

Details

Only the biotypes that are likely to have a promoter will be filtered in. This is currently hardcoded in the function; see its source code. Example of biotypes without a promoter: VDJ segments, etc.

Value

A Run-length-encoded (Rle) factor of same length as the GRanges object, indicating if the interval is promoter, exon, intron or unknown, or just promoter, gene, unknown if the type metadata is absent.

Author(s)

Charles Plessy

See Also

CTSScoordinatesGR, exampleZv9_annot

Other CAGEr annotation functions: annotateCTSS, plotAnnot, ranges2genes, ranges2names

Examples

CAGEr:::ranges2annot(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)


[Package CAGEr version 1.22.3 Index]