disjointExons: Extract non-overlapping exon parts from an object

In GenomicFeatures: Conveniently import and query gene models

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WARNING: disjointExons is superseded by exonicParts and will be deprecated soon.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

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
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    'browseVignettes()'. To cite Bioconductor, see
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GenomicFeatures documentation built on April 2, 2021, 6 p.m.