RunMiXCRseq: RunMiXCRseq

View source: R/RMiXCR_runners.R

RunMiXCRseqR Documentation

RunMiXCRseq

Description

It runs MiXCR for RNAseq data according to MiXCR main page advise. In this implementation it runs first RunMiXCRseqAlignment and the RunMiXCRseqClones one after the other. See the other helps for more details

Usage

RunMiXCRseq(sbj, species = c("hsa","mmu"), extendedAlignments = TRUE )

Arguments

sbj

sbj (character) The full path name of the sbj.R1.fastq file (the paired read file should be named as sbj.R2.fastq)

species

character any of "hsa","mmu" (default hsa)

extendedAlignments

default FALSE,

Value

if success, the it builds three files sbj.alignments.vdjca and sbj.clones.clns and clones.xlsx and return a vector with the full path to files #' if fail, returns NA

Examples

/dontrun{
      subj.file <- "/home/.../subject.R1.fastq"
      out.vdja.and.clone.files <- RunMiXCRseq(sbj = subj.file)
      print(out.vdja.and.clone.files[1])#vdja file path
      print(out.vdja.and.clone.files[2])#clones file path
      print(out.vdja.and.clone.files[3])#clones excel report file path
}

elmerfer/RMiXCR documentation built on May 27, 2023, 5:08 a.m.