mergePerGroup {BaalChIP} | R Documentation

## Method mergePerGroup

### Description

Merges all ChIP-seq datasets within a group of samples creating a data.frame that contains allele-specific read count data for all variants that need to be analysed.

### Usage

    mergePerGroup(.Object)

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

### Arguments

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

### Details

if QCfilter has been applied, will use the most up-to-date variant set available for each individual BAM file (after QC). Missing values are allowed for heterozygous variants that are not available (e.g. do not pass filter for a particular ChIP-seq dataset).

### Value

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

### 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))

    res <- mergePerGroup(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 1.20.0 Index]