countFeatures: count reads

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

Description

function assay reads by V, J or V-J genes.

Usage

countFeatures(x, level = c("VpJ", "V", "J", "VJ", "CDR3aa"))

Arguments

x	an object of class [RepSeqExperiment]
level	"V", "J" or "VJ" genes.

Value

a data.table of assay with unique features in rows and samples in columns.

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
cts <- countFeatures(x = dataset, level = "VJ")
cts

## End(Not run)

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