common_regions: Find common genomic regions across several samples

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Find common genomic regions across several samples

Usage

common_regions(gr_list, min_width = 0, min_coverage = floor(length(gr_list)/4), gap = 0.5)

Arguments

gr_list	a list of GRanges
min_width	minimal width of the common regions
min_coverage	minimal cross-sample coverage for the common regions
gap	gap to merge common regions, pass to reduce2

Details

A common region is defined as a region which covers in at least k samples. The output can be sent to subgroup_specific_genomic_regions to find subgroup specific regions.

Value

A GRanges object contains coordinates of common regions. The columns in meta data are percent of the common region which is covered by regions in every sample.

Author(s)

Zuguang Gu <[e-mail]>

See Also

The returned variable can be sent to subgroup_specific_genomic_regions to find subgroup specific regions.

Examples

gr_list = list(
    gr1 = GRanges(seqnames = "chr1", ranges = IRanges(1, 8)),
    gr2 = GRanges(seqnames = "chr1", ranges = IRanges(3, 9)),
    gr3 = GRanges(seqnames = "chr1", ranges = IRanges(2, 7)),
    gr4 = GRanges(seqnames = "chr1", ranges = IRanges(c(1, 6), c(4, 10))),
    gr5 = GRanges(seqnames = "chr1", ranges = IRanges(c(1, 9), c(3, 10)))
)
common_regions(gr_list, min_coverage = 4, gap = bp(1))
common_regions(gr_list, min_coverage = 4, gap = 0.5)

eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.