BaalChIP.run {BaalChIP} | R Documentation

## Method BaalChIP.run

### 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

    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

    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)

[Package BaalChIP version 1.12.0 Index]