This function simply runs ChIPQC on a sample sheet and
returns QC metrics. It generates a consensus peakset between all sets by
retaining and merging all peaks that overlap in at least two samples before
defining the fraction of reads in peaks and other metrics.
RunChIPQC(outpath, samplesheet, chromosomes = "chr18")
| outpath | Path to directory to be used for output. |
|---|---|
| samplesheet | Path to samplesheet containing sample metadata. |
| chromosomes | String or character vector indicating chromosomes to be used for QC. |
Dataframe containing QC metrics for each sample, including cross-correlation scores, fraction of reads in peaks, fragment length, etc.
A basic plot showing overlap between peaksets will also be generated, which
can be useful for defining how many samples a peak should be found in to be
included in the consensus peakset as defined in RunDiffBind.