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

In pmoulos/metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

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.

Author(s)

Panagiotis Moulos

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)

pmoulos/metaseqR documentation built on Dec. 21, 2020, 6:19 a.m.