getOverlaps: get shared clonotypes

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

Description

function returns an RepSeqExperiment object containing shared clonotyes which expressed in at least two samples

Usage

getOverlaps(x, level = c("VpJ", "CDR3dna"), libnames = NULL)

Arguments

x	an object of class [RepSeqExperiment]
level	level of shared clonotypes, VpJ or CDR3dna
libnames	a vector of specific sample names to get shared clonotypes, default value is NULL, shared clonotypes will be computed for all samples.

Value

an object of class [RepSeqExperiment]

Examples

## Not run: 
# The package RepSeqData contains example datasets 
library(RepSeq)
library(RepSeqData)
rownames(sData(RepSeqData))
# get overlap clonotypes between the sample S01 and the sample S02 
overlapClones <- getOverlaps(RepSeqData, 
                           level = "VpJ", 
                           libnames=("S01", "S02")) 
overlapClones

## End(Not run)

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