findFeatureComb-methods: Find combitations of genomic features

In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

Description

Provided a GRangesList, finds the combinations of sets of ranges. It is mostly used to look at the combinatorics of transcription factor binding. The function works by, firstly, constructing a union of all ranges in the list, which are then designated by the combinatorics of overlap with the original sets. A caveat of this approach is that the number of possible combinations increases exponentially, so we would advise you to use it with up to 6 data sets. If you wish to take a look at a greater number of factors, methods like self organizing maps or ChromHMM might be more appropriate.

Usage

findFeatureComb(gl, width=0, use.names=FALSE, collapse.char=':')

## S4 method for signature 'GRangesList'
findFeatureComb(gl, width = 0, use.names = FALSE,
  collapse.char = ":")

Arguments

gl	a GRangesList object, containing ranges for which represent regions enriched for transcription factor binding
width	integer is the requested width of each enriched region. If 0 the ranges are not resized, if a positive integer, the width of all ranges is set to that number. Ranges are resized relative to the center of original ranges.
use.names	a boolean which tells the function whether to return the resulting ranges with a numeric vector which designates each class (the default), or to construct the names of each class using the names from the GRangesList
collapse.char	a character which will be used to separate the class names if use.names=TRUE. The default is ':'

Value

a GRanges object

Examples

library(GenomicRanges)
g = GRanges(paste('chr',rep(1:2, each=3), sep=''), IRanges(rep(c(1,5,9), times=2), width=3))
gl = GRangesList(g1=g, g2=g[2:5], g3=g[3:4])
findFeatureComb(gl)
findFeatureComb(gl, use.names=TRUE)

BIMSBbioinfo/genomation documentation built on March 13, 2020, 5:28 a.m.