disjointExons extracts the non-overlapping exon parts from a
TxDb object or any other supported object.
disjointExons(x, ...)
"disjointExons"(x, aggregateGenes=FALSE, includeTranscripts=TRUE, ...)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.
disjointExons : A logical. When TRUE
(default) a tx_name metadata column is included that
lists all transcript names that overlap the exon fragment.
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.
transcripts, transcriptsBy, and
transcriptsByOverlaps for the core genomic features
extractors.