segmentUsage: compute usage of segments

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

Description

This function computed clonotype usage

Usage

segmentUsage(x, level = c("VpJ", "V", "J", "VJ"))

Arguments

x	an object of class [RepSeqExperiment], returned by readClonotypeSet
level	segment usage (ie percentage) of VpJ, V, J, or VJ within a repertoire.

Value

a data.table of segment usage of genes in each repertoire.

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) 
dataset <- readClonotypeSet(fileList = l, 
                   cores=1L, 
                   aligner = "MiXCR", 
                   chain = "B", 
                   sampleinfo = sampleData, 
                   keep.ambiguous=FALSE, 
                   keep.unproductive=FALSE, 
                   aa.th=8)
dataset
# produce a count matrix of VJ
seg.use <- segmentUsage(x = dataset, level = "VJ")
seg.use

## End(Not run)

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