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WARNING: `disjointExons` is superseded by `exonicParts` and will be deprecated soon.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.

### See Also

`exonicParts` for an improved version of `disjointExons`.

### Examples

    ## TODO

[Package GenomicFeatures version 1.40.1 Index]