BaalChIP.run {BaalChIP}

R Documentation

Method BaalChIP.run

Description

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.

Usage

BaalChIP.run(.Object, cores = 4, verbose = TRUE)

## S4 method for signature 'BaalChIP'
BaalChIP.run(.Object, cores = 4, verbose = TRUE)

Arguments

.Object	An object of the BaalChIP class.
cores	number of cores for parallel computing (default is 4).
verbose	logical. If TRUE reports extra information on the process

Details

This function is a wrapper of the following functions: alleleCounts, QCfilter, mergePerGroup, filter1allele, getASB

Value

An object of the BaalChIP class.

Author(s)

Ines de Santiago

See Also

summaryQC, plotQC

Examples

samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP")  
hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"), 
         "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP"))
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)

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