getTranscriptGcAndWidth: Gets GC proportions and gene widths

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Gets GC proportions and gene widths

Description

Gets GC proportions and gene widths from annotation (gtf or gff) and sequence (fasta) information.

Usage

getTranscriptGcAndWidth(param = NULL, genomeFn = NULL, featureFn = NULL)

Arguments

param

the parameters to load the annotation and sequence files from.

Value

Returns a list containing named vectors for the GC proportion and the gene width.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

ezLoadFeatures

readDNAStringSet

Views

letterFrequency

Examples

param = ezParam()
param$ezRef@refFeatureFile = system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE)
fp = "/srv/GT/reference/Saccharomyces_cerevisiae/Ensembl/EF4/Sequence/WholeGenomeFasta/genome.fa"
param$ezRef@refFastaFile = fp
gw = getTranscriptGcAndWidth(param)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.