QCfilter {BaalChIP} | R Documentation

## Method QCfilter

### Description

Quality control step for removing variants that may be problematic for identification of allele-specific events.

### Usage

    QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE)

    ## S4 method for signature 'BaalChIP'
    QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE)

### Arguments

`.Object` | An object of the `BaalChIP` class.
`RegionsToFilter` | a named list of GRanges objects. Variants overlapping these regions will be removed.
`RegionsToKeep` | a named list of GRanges objects. Works in an oposite way to 'RegionstoFilter', variants NOT overlapping these regions will be removed.
`verbose` | logical. If TRUE reports extra information on the process

### Value

An updated `BaalChIP` object with the slot `alleleCounts` containing a list of GRanges objects that pass filters.

### Author(s)

Ines de Santiago

### See Also

`BaalChIP.get`, `plotQC`, `summaryQC`

### 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 <- alleleCounts(res, min_base_quality=10, min_mapq=15)
    data('blacklist_hg19')
    data('pickrell2011cov1_hg19')
    data('UniqueMappability50bp_hg19')
    res <- QCfilter(res,
                   RegionsToFilter=list('blacklist'=blacklist_hg19,
                   'highcoverage'=pickrell2011cov1_hg19),
                   RegionsToKeep=list('UniqueMappability'=UniqueMappability50bp_hg19))

    #check results
    plotQC(res,'barplot')
    summaryQC(res)

[Package BaalChIP version 1.18.0 Index]