Extract non-overlapping exon parts from an object
disjointExons extracts the non-overlapping exon parts from a
TxDb object or any other supported object.
WARNING: disjointExons is superseded by exonicParts
and will be deprecated soon. Please use improved exonicParts
instead.
disjointExons(x, ...)
## S4 method for signature 'TxDb'
disjointExons(x, aggregateGenes=FALSE,
includeTranscripts=TRUE, ...)x |
A TxDb object or any other supported object. |
... |
Arguments to be passed to methods. |
aggregateGenes |
For |
includeTranscripts |
For |
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.
A GRanges object.
disjointExons was originally implemented by Mike Love and Alejandro
Reyes and then moved (and adapted) to GenomicFeatures by Valerie
Obenchain.
exonicParts for an improved version of disjointExons.
## TODO
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