reduce2: Merge genomic regions

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

Description

Merge genomic regions

Usage

reduce2(gr, max_gap = 1000, gap = bp(1000), add_n_column = TRUE)

Arguments

gr	a GRanges object
max_gap	maximum gap to merge, measured in base pairs. Only work if gap is the ratio.
gap	a numeric value means to extend each region by gap times of its width before merging. If gap represents number of base pairs, use bp, kb or mb to wrap it. If gap represents absolute number of base pairs, the functionality is same as reduce.
add_n_column	whether to add a column which represents number of regions merged, used internally.

Details

reduce only merges regions with fixed gap width, but sometimes it is not reasonable to set gap to a same width for all regions. Assuming we have a list of differentially methylated regions (DMRs) and we want to reduce the number of DMRs by merging neighouring DMRs. DMRs distribute differently in different places in the genome, e.g. DMRs are dense and short in CpG-rich regions (e.g. CpG islands) while long in CpG-sparse regions (e.g. gene bodies and intergenic regions), thus the merging should be applied based to the width of every DMR itself. reduce2 can merge regions by the width of every region itself. This type of merging is dynamic because after each iteration of merging, width and number of regions change which results in changing of extension of some regions. The whole merging will proceed iteratively unless there is no new merging or the gap between regions reaches max_gap.

If there are numeric meta columns, corresponding values will be summed up for the merged regions. There will be a new column .__n__. added which represents number of regions that are merged.

Value

a GRanges object.

Author(s)

Zuguang Gu <[e-mail]>

Examples

gr = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 4, 8 ,12), 
    end = c(2, 5, 10, 20)))
reduce2(gr, gap = bp(2))
reduce2(gr, gap = 0.1)

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