BaalChIP.run {BaalChIP} | R Documentation |
Method BaalChIP.run
BaalChIP.run is a wrapper convenience function, to compute allele counts and perform quality controls in one step. This function will use the package's defaults.
BaalChIP.run(.Object, cores = 4, verbose = TRUE) ## S4 method for signature 'BaalChIP' BaalChIP.run(.Object, cores = 4, verbose = TRUE)
.Object |
An object of the |
cores |
number of cores for parallel computing (default is 4). |
verbose |
logical. If TRUE reports extra information on the process |
This function is a wrapper of the following functions: alleleCounts
, QCfilter
, mergePerGroup
, filter1allele
, getASB
An object of the BaalChIP
class.
Ines de Santiago
setwd(system.file('test',package='BaalChIP')) samplesheet <- 'exampleChIP.tsv' hets <- c('MCF7'='MCF7_hetSNP.txt', 'GM12891'='GM12891_hetSNP.txt') res <- BaalChIP(samplesheet=samplesheet, hets=hets) res <- BaalChIP.run(res, cores=2) #summary of the QC step summaryQC(res) #summary of the ASB step summaryASB(res)