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))