RunMiXCR: RunMiXCR

In elmerfer/RMiXCR: An easy wrapper for MiXCR software

RunMiXCR

Description

RunMiXCR

Usage

## Not run: 
fasta.file <- "/home/mysubjects/subject1.R1.fastq"
RunMiXCR(sbj=fasta.file, 
         species="hsa", #human
         assemblePartial=FALSE, 
         extendedAlignments=FALSE, 
         nThreads = 6L #six cores
         )


## End(Not run)

Arguments

sbj	(character) The full path name of the sbj.R1.fastq file (the paired read file should be named as sbj.R2.fastq)
species	any of "hsa","mmu" (human - mouse)
assemblePartial	(logical, default FALSE) if partial read should be assembled (Perform two rounds of contig assembly)
extendedAlignments	(logical, default TRUE) if TCR extension alignment should be performed (in case of incomplete TCR alignments)
nThreads	(integer) number of cores

Value

a list with clones, vmin, vdetails.clones, TRA.clones,TRB.clones,TRG.clones,TRD.clones data frames it also save an Excel file as full.path.sbj.alignments.vdjca.xlsx

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