DataPreparation_TCR_MiXCR: MiXCR workflow.

In masato-ogishi/Repitope: Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling

MiXCR workflow.

Description

MiXCR_Script generates MiXCR script.
MiXCR_CombineClonotypes reads and combines MiXCR-derived clonotypes. Note: Only TCR beta chains are retained.

Usage

MiXCR_Script(
  dir = "C:/SRA/output",
  mixcrPath = "C:/MiXCR/",
  javaMaxMemory = "60G",
  rnaseq = F,
  species = "hsa"
)

MiXCR_CombineClonotypes(
  dirClones = NULL,
  clonesFileNames = NULL,
  countSummarise = F,
  rdsFileName = NULL
)

Arguments

dir	A directory in which FASTQ files are stored.
mixcrPath	A path to MiXCR JAR file.
javaMaxMemory	A maximum memory size allocated to the Java virtual machine.
rnaseq	Logical. Specifies if the analysis takes RNASeq datasets.
species	A character string. "hsa" or "mmu".
dirClones	A directory in which MiXCR clonotype TXT files are stored.
clonesFileNames	(Optional) Alternativey, MiXCR clonotype TXT filenames can be provided as a list.
countSummarise	Logical. If True, the number of datasets containing each CDR3 sequence is counted. If False, raw SRA accessions are provided as such.
rdsFileName	(Optional) A filename to which the clonotype summary table is saved as an RDS file.

masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.