reduce.exons {metaseqR} | R Documentation

## Merges exons to create a unique set of exons for each gene

### Description

This function uses the `"reduce"` function of IRanges to construct virtual unique exons for each gene, so as to avoid inflating the read counts for each gene because of multiple possible transcripts. If the user wants transcripts instead of genes, they should be supplied to the original annotation table.

### Usage

        reduce.exons(gr, multic = FALSE)

### Arguments

`gr` | a GRanges object created from the supplied annotation (see also the `read2count` and `get.annotation` functions.
`multic` | a logical value indicating the presence of multiple cores. Defaults to `FALSE`. Do not change it if you are not sure whether package parallel has been loaded or not.

### Value

A GRanges object with virtual merged exons for each gene/transcript.

### Author(s)

Panagiotis Moulos

### Examples

        require(GenomicRanges)
        multic <- check.parallel(0.8)
        ann <- get.annotation("mm9","exon")
        gr <- makeGRangesFromDataFrame(
            df=ann,
            keep.extra.columns=TRUE,
            seqnames.field="chromosome"
        )
        re <- reduce.exons(gr,multic=multic)

[Package metaseqR version 1.28.0 Index]