metaseqR (version 1.12.2)

reduce.gene.data: Reduce the gene annotation in case of not all chromosomes present in counts

Description

This function reduces the gene annotation in case of exon reads and when the data to be analyzed do not contain all the standard chromosomes of the genome under investigation. This can greatly reduce processing time in these cases.

Usage

reduce.gene.data(exon.data, gene.data)

Arguments

exon.data

the exon annotation already reduced to the size of the input exon counts table.

gene.data

an annotation data frame from the same organism as exon.counts (such the ones produced by get.annotation).

Value

• The gene.data annotation, reduced to have the same chromosomes as in exon.data, or the original gene.data if exon.data do contain the standard chromosomes.

Examples

data("hg19.exon.data",package="metaseqR")
gene.data <- get.annotation("hg19","gene","ensembl")
reduced.gene.data <- reduce.gene.data(hg19.exon.counts,
    gene.data)