Define Regions Among Overlaps

DefineRegions(overlaps.all, sample = NULL, regions = NULL)

Arguments

overlaps.all

Output from VennPeaks with return.overlaps.all set to TRUE provides matrix with columns Sample, PeakID, and matrix of intersections

sample

Primary sample of interest, used as the reference; must match one of the column names from overlaps.all

regions

vector of present/absent for columns, e.g. for 3 cols: assuming first column is passed as sample parameter: c(0, 1, 1) = three-way intersection (your sample is set to 0 in matrix) c(0, 1, 0) = two-way intersection with your sample + column 2 c(0, 0, 0) = unique to your sample This returns only the STRICT intersection (does not consider all cases); so to get all relevant peakIDs you may need to do several DefineRegions runs

Value

PeakID for your reference sample of given overlaps, as denoted by regions

Examples

## Run VennPeaks to retrieve overlaps.all matrix
vpo.t <- VennPeaks(rp.e, return.overlaps.all = TRUE)
## returns three-way intersect assuming column 1 is k27ac.TE
DefineRegions(vpo.t, "k27ac.TE", c(0, 1, 1))