getKallistoReference: Builds and gets a kallisto reference
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

getKallistoReference

R Documentation

Builds and gets a kallisto reference

Description

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

Usage

  getKallistoReference(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.

Value

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

Author(s)

Roman Briskine

Examples

  ## Not run: 
    GENOMES_ROOT <- "/home/gtan/analysis/gtan/referenceFiles"
    Sys.setenv("PATH"=paste("/usr/local/ngseq/packages/Aligner/kallisto/0.43.1/bin",
                            Sys.getenv("PATH"), sep=":"))
    param <- list()
    param[['transcriptTypes']] = 'protein_coding,rRNA'
    param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-08-11'
    param <- ezParam(param)
    getKallistoReference(param)
  
## End(Not run)

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