parseClonotypeR: parse ClonotypeR tables

In ph-pham/RepSeq: Analysis of High-throughput sequencing repertoire data (RepSeqTools)

Description

function imports clonotype tables produced by ClonotypeR aligner.

Usage

parseClonotypeR(path, chain = c("A", "B"))

Arguments

path	full path to a TSV file returned by ClonotypeR (tab-delimited text file, could be gzipped).
chain	TCR chain A or [codeB to extract. Default value is A.

Value

a data.table having 7 columns. lib name of the repertoire, V V gene identification, J J gene identification, CDR3aa CDR3aa chain, CDR3dna CDR3 DNA chain, score mapq quality score, count clonotype assay. Clonotypes were deleted if CDR3aa chain contains STOP codon (*), CDR3dna length is not divisible by 3 or CDR3dna chain contains base "N".

Examples

## Not run: 
dataset <- parseClonotypeR(path, chain="B")

## End(Not run)

ph-pham/RepSeq documentation built on Dec. 22, 2021, 7:47 a.m.