computeGeneLength: Extracting the gene length from annotations

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Extracting the gene length from annotations

Description

Computes the length for each gene based on the given GTF file or annotation. Here the length of a gene is defind by the total number of bases covered by exons.

Usage

computeGeneLength(ods, gtfFile, format = "gtf", mapping = NULL, ...)

Arguments

ods	An OutriderDataSet for which the gene length should be computed.
gtfFile	Can be a GTF file or an txDb object with annotation.
format	The format parameter from makeTxDbFromGFF
mapping	If set, it is used to map gene names between the GFT and the ods object. This should be a 2 column data.frame: 1. column GTF names and 2. column ods names.
...	further arguments to makeTxDbFromGFF

Value

An OutriderDataSet containing a basepairs column with the calculated gene length. Accessable through mcols(ods)['baisepairs']

Examples

ods <- makeExampleOutriderDataSet(dataset="GTExSkinSmall")
annotationFile <- system.file("extdata", "gencode.v19.genes.small.gtf.gz",
        package="OUTRIDER")
ods <- computeGeneLength(ods, annotationFile)

mcols(ods)['basepairs']
fpkm(ods)[1:10,1:10]

gagneurlab/OUTRIDER documentation built on April 19, 2024, 12:20 a.m.