GenomicFeatures (version 1.24.4)

disjointExons: Extract non-overlapping exon parts from an object

Description

disjointExons extracts the non-overlapping exon parts from a TxDb object or any other supported object.

Usage

disjointExons(x, ...)
"disjointExons"(x, aggregateGenes=FALSE, includeTranscripts=TRUE, ...)

Arguments

x
A TxDb object or any other supported object.
...
Arguments to be passed to methods.
aggregateGenes
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.

Value

A GRanges object.

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.

See Also

Examples

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