filter1allele {BaalChIP} | R Documentation

## Method filter1allele

### Description

Method filter1allele

Filters the data frame available within a `BaalChIP` object (slot `mergedCounts`). This filter ignores variants for which only one allele is observed after pooling ChIP-seq reads from all datasets.

### Usage

    filter1allele(.Object)

    ## S4 method for signature 'BaalChIP'
    filter1allele(.Object)

### Arguments

`.Object` | An object of the `BaalChIP` class.

### Value

An updated `BaalChIP` object with the slot `mergedCounts` containing a data.frame of merged samples per group with variants that pass the filter.

### Author(s)

Ines de Santiago

### See Also

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

### 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 <- 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))

    res <- mergePerGroup(res)
    res <- filter1allele(res)

    #retrieve mergedCounts:
    counts <- BaalChIP.get(res, 'mergedCounts')

    #mergedCounts are grouped by group_name:
    names(counts)
    sapply(counts, dim)

    #check out the result for one of the groups:
    head(counts[[1]])

[Package BaalChIP version 1.16.0 Index]