readClonotypes: read clonotype table

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

Description

function readColontypes is a wrapper of parseClonotypes & filterClonotypes

Usage

readClonotypes(
  path,
  aligner = c("MiXCR", "Adaptive", "rTCR", "ClonotypeR"),
  chain = c("A", "B"),
  keep.ambiguous = FALSE,
  keep.unproductive = FALSE,
  aa.th = 8,
  outFiltered = F
)

Arguments

path	a path to a clonotype file, for the moment, only TSV from ClonotypeR is supported.
aligner	choice between type of input file provided by "Adaptive", "ClonotypeR", "MiXCR", "rTCR". Default is "MiXCR".
chain	a character A or B indicating the chain to be imported. Default is A.
keep.ambiguous	a boolean choice if ambiguous clonotypes (contain STOP codon) should be kept in analysis. Default is FALSE.
keep.unproductive	a boolean choice if unproductive clonotypes (Euclidean dividion of aa length by 3 > 0) should be kept in analysis. Default is FALSE.
aa.th	an interger indicates the maximal number of amino acids could be deviated from the mean length. Default is 8.
outFiltered	write dropped reads to file. Default folder is getwd().

Value

a filtered clonotype table.

See Also

parseClonotypeR, filterClonotypes

Examples

## Not run: 
# The package RepSeqData contains example datasets 
l <- list.files(system.file(file.path('extdata/mixcr'), 
                         package = 'RepSeqData'), 
                         full.names = TRUE)
l
# first element of the vector
path <- l[1]
dataset <- readClonotypes(path = path, 
                   aligner = "MiXCR", 
                   chain = "B", 
                   keep.ambiguous=FALSE, 
                   keep.unproductive=FALSE, 
                   aa.th=8, 
                   outFiltered=F)
dataset

## End(Not run)

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