R: Prepare annotation transcriptDb object for DEXSeq.

prepareAnnotationForDEXSeq-deprecated {DEXSeq}

R Documentation

Prepare annotation transcriptDb object for DEXSeq.

Description

WARNING: This function is deprecated and it has been replaced by the function disjointExons, from the package GenomicFeatures.

Usage

prepareAnnotationForDEXSeq( transcriptDb, aggregateGenes=FALSE, includeTranscripts=TRUE )

Arguments

`transcriptDb`	An transcriptDb object.
`aggregateGenes`	Logical. Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored.
`includeTranscripts`	Logical. Indicates whether the transcript information of each exon should be added.

Value

A GRanges object.

Author(s)

From code kindly provided by Mike Love.

Examples

## Not run: 
   library(GenomicFeatures)
   hse <- makeTranscriptDbFromBiomart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
   exonicParts <- prepareAnnotationForDEXSeq( hse )

## End(Not run)

[Package DEXSeq version 1.8.0 Index]