For disjointExons : A logical. When FALSE
(default) exon fragments that overlap multiple genes are dropped.
When TRUE, all fragments are kept and the gene_id
metadata column includes all gene ids that overlap the exon fragment.
includeTranscripts
For disjointExons : A logical. When TRUE
(default) a tx_name metadata column is included that
lists all transcript names that overlap the exon fragment.
Details
disjointExons creates a GRanges of
non-overlapping exon parts with metadata columns of gene_id and exonic_part.
Exon parts that overlap more than 1 gene can be dropped with
aggregateGenes=FALSE. When includeTranscripts=TRUE
a tx_name metadata column is included that lists all
transcript names that overlap the exon fragment. This function
replaces prepareAnnotationForDEXSeq in the DEXSeq
package.
Value
A GRanges object.
Author(s)
disjointExons was originally implemented by Mike Love and Alejandro
Reyes and then moved (and adapted) to GenomicFeatures by Valerie
Obenchain.
See Also
transcripts, transcriptsBy, and
transcriptsByOverlaps for the core genomic features
extractors.