getTranscriptSequences: Gets transcript sequences

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

Gets transcript sequences

Description

Gets transcript sequences from annotation (gtf or gff) and sequence (fasta) information.

Usage

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

Arguments

param	the parameters to load the annotation and sequence files from.
genomeFn	character(1): filepath of the genome assembly fasta file.
featureFn	character(1): filepath of the gtf annotation file.

Details

‘genomeFn’ and ‘featureFn’ are determined from ‘param’ when available.

Value

Returns an object of the class DNAStringSet.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

  ## Not run: 
    genomeFn <- "/srv/GT/reference/Saccharomyces_cerevisiae/Ensembl/EF4/Sequence/WholeGenomeFasta/genome.fa"
    featureFn <- "/srv/GT/reference/Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Genes/genes.gtf"
    ts1 <- getTranscriptSequences(genomeFn=genomeFn, featureFn=featureFn)
    
    param = ezParam()
    param$ezRef@refFeatureFile = featureFn
    param$ezRef@refFastaFile = genomeFn
    ts2 <- getTranscriptSequences(param)
  
## End(Not run)

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