View source: R/RMiXCR_runners.R
RunMiXCRseq | R Documentation |
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
RunMiXCRseq(sbj, species = c("hsa","mmu"), extendedAlignments = TRUE )
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, |
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
/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
}
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