addNewSamples: Extends an exisiting qseaSet by new samples

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Extends an exisiting qseaSet by new samples

Description

This function allows the qseaSet to be extended by new samples, provided in the sample table.

Usage

addNewSamples(qs, sampleTable, force=FALSE, parallel=FALSE)

Arguments

qs	The qseaSet object to be extended
sampleTable	data.frame, describing the samples. Must be in same format as getSampleTable(qs)
force	force adding of new samples, even if existing CNV or enrichment information requires recomputation
parallel	parallel processing of alignment files

Value

An object of class qseaSet, including the new samples.

Author(s)

Mathias Lienhard

Examples

library("BSgenome.Hsapiens.UCSC.hg19")
data(samplesNSCLC, package="MEDIPSData")
path=system.file("extdata", package="MEDIPSData")
samples_NSCLC$file_name=paste0(path,"/",samples_NSCLC$file_name )
originalQseaSet=createQseaSet(sampleTable=samples_NSCLC[1:4,], 
        BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", 
        window_size=500)
originalQseaSet=addCoverage(originalQseaSet, uniquePos=TRUE, paired=TRUE)
qseaSet=addNewSamples(originalQseaSet, samples_NSCLC)

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.