R: Extract non-overlapping exon parts from an object

disjointExons {GenomicFeatures}

R Documentation

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.

WARNING: disjointExons is superseded by exonicParts and will be deprecated soon. Please use improved exonicParts instead.

Usage

disjointExons(x, ...)

## S4 method for signature 'TxDb'
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.

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.

Examples

## TODO

[Package GenomicFeatures version 1.40.1 Index]