RunChIPQC: Run ChIPQC on a sample sheet
In j-andrews7/OneLinerOmics: One-liner RNA-seq and ChIP-seq Analyses

Description Usage Arguments Details Value Author(s) See Also

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.

1	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.

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.

Dataframe containing QC metrics for each sample, including cross-correlation scores, fraction of reads in peaks, fragment length, etc.

Jared Andrews

ChIPQC

j-andrews7/OneLinerOmics documentation built on Sept. 9, 2021, 11 a.m.