RepSeqExp: build RepSeqExperiment object from clonotype tables

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

Description

function creates RepSeqExperiment object from clonotype tables.

Usage

RepSeqExp(clonotypetab, sampleinfo = NULL)

Arguments

clonotypetab	a data.table of clonotype tables. The column names should be: lib, V, J, CDR3aa, CDR3dna, VpJ, VJ, score, count.
sampleinfo	a data frame containing sample meta data

Value

an object of class RepSeqExperiment

Examples

## Not run: 
# The package RepSeqData contains example datasets 
l <- list.files(system.file(file.path('extdata/mixcr'), 
                     package = 'RepSeqData'), 
                     full.names = TRUE)
l# list of gz-compressed files 
sampleData <- read.table(system.file(file.path('extdata/sampledata.txt'), 
                     package='RepSeqData'), 
                     sep = "\t", 
                     row.names = 2) 
clontab.tmp <- lapply(l, readClonotypes, aligner="MiXCR")
clontab <- data.table::rbindlist(dataset.tmp)
dataset <- RepSeqExp(clontab, sampleinfo = sampleData)
dataset

## End(Not run)

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