makeConsensus: Make a set of consensus peaks

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Make a set of consensus peaks

Description

Make a set of consensus peaks based on the number of replicates

Usage

makeConsensus(
  x,
  p = 0,
  var = NULL,
  method = c("union", "coverage"),
  ignore.strand = TRUE,
  simplify = FALSE,
  min_width = 0,
  merge_within = 1L,
  ...
)

Arguments

x	A GRangesList
p	The minimum proportion of samples (i.e. elements of x) required for a peak to be retained in the output. By default all merged peaks will be returned
var	Additional columns in the mcols element to retain
method	Either return the union of all overlapping ranges, or the regions within the overlapping ranges which are covered by the specified proportion of replicates. When using p = 0, both methods will return identical results
ignore.strand, simplify, ...	Passed to reduceMC or intersectMC internally
min_width	Discard any regions below this width
merge_within	Passed to reduce as min.gapwidth

Details

This takes a list of GRanges objects and forms a set of consensus peaks.

When using method = "union" the union ranges of all overlapping peaks will be returned, using the minimum proportion of replicates specified. When using method = "coverage", only the regions within each overlapping range which are 'covered' by the minimum proportion of replicates specified are returned. This will return narrower peaks in general, although some artefactual very small ranges may be included (e.g. 10bp). Careful setting of the min_width and merge_within parameters may be very helpful for these instances. It is also expected that setting method = "coverage" should return the region within each range which is more likely to contain the true binding site for the relevant ChIP targets

Value

GRanges object with mcols containing a logical vector for every element of x, along with the column n which adds all logical columns. These columns denote which replicates contain an overlapping peak for each range

If any additional columns have been requested using var, these will be returned as CompressedList objects as produced by reduceMC() or intersectMC().

See Also

reduceMC intersectMC

Examples

data("peaks")
## The first three replicates are from the same treatment group
grl <- peaks[1:3]
names(grl) <- gsub("_peaks.+", "", names(grl))
makeConsensus(grl)
makeConsensus(grl, p = 2/3, var = "score")

## Using method = 'coverage' finds ranges based on the intersection
makeConsensus(grl, p = 2/3, var = "score", method = "coverage")

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.