computeGeneLength {OUTRIDER} | R Documentation |
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.
computeGeneLength(ods, gtfFile, format = "gtf", mapping = NULL, ...)
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 |
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 |
An OutriderDataSet containing a basepairs
column with the
calculated gene length. Accessable through
mcols(ods)['baisepairs']
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]