ranges2annot {CAGEr} | R Documentation |
Assigns region types such as promoter, exon or unknown to CTSSes.
ranges2annot(ranges, annot)
ranges |
The CTSS (GRanges) object, for example extracted from a
RangedSummarizedExperiment object with the |
annot |
A |
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.
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.
Charles Plessy
CTSScoordinatesGR
, exampleZv9_annot
Other CAGEr annotation functions: annotateCTSS
,
plotAnnot
, ranges2genes
,
ranges2names
CAGEr:::ranges2annot(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)