getRSEMReference: Builds and gets a RSEM reference

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

Builds and gets a RSEM reference

Description

Builds and gets a RSEM reference by returning the file path to it.

Usage

  getRSEMReference(param)

Arguments

param

a list of parameters: transcriptFasta an optional character specifying the path to a fasta file. If specified, the reference will be prepared using it. ezRef@refIndex a character specifying the location of the index that is used in the alignment. ezRef@refFeatureFile a character specifying the path to the annotation feature file (.gtf). ezRef@refFastaFile a character specifying the path to the fasta file. transcriptTypes character(n): an optional list of transcript types to select to build the indices.

Value

Returns a character specifying the file path to the RSEM indexed reference genome.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

  ## Not run: 
    GENOMES_ROOT <- "/home/gtan/analysis/gtan/referenceFiles"
    Sys.setenv("PATH"=paste("/usr/local/ngseq/packages/Aligner/RSEM/1.3.0/bin",
                            "/usr/local/ngseq/packages/Aligner/Bowtie/1.1.2/bin",
                            Sys.getenv("PATH"), sep=":"))
    param <- list()
    param[['transcriptTypes']] = 'protein_coding,rRNA,tRNA,Mt_rRNA,Mt_tRNA'
    param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-08-11'
    param <- ezParam(param)
    getRSEMReference(param)
  
## End(Not run)
  ls = list('refBuild' = 'Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Version-2013-03-07')
  param = ezParam(userParam = ls)
  getRSEMReference(param)

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.