Method BaalChIP.run

Share:

Description

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.

Usage

1
2
3
4
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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)