findFeatureComb {genomation} | R Documentation |
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.
findFeatureComb(gl, width=0, use.names=FALSE, collapse.char=':') ## S4 method for signature 'GRangesList' findFeatureComb(gl, width = 0, use.names = FALSE, collapse.char = ":")
gl |
a |
width |
|
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 ':' |
a GRanges object
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)