# CallRegions: Call and merge regions using joint posterior probabilities... In BAC: Bayesian Analysis of Chip-chip experiment

## Description

Call and merge regions using joint posterior probabilities calculated by BAC.

## Usage

 `1` ```CallRegions(position,jointPP,cutoff=0.5,maxGap=500) ```

## Arguments

 `position` A vector containing the probe genomic positions `jointPP` A vector containing the joint posterior probabilities as returned by BAC. `cutoff` The cutoff used to call regions. `maxGap` The maximum gap allowed between regions. Regions that are less than maxGap bps away will be merged.

## Value

A vector containing the region index for each probe. Probes with the same positive index belong to the same region, whereas probe with index zero are background probes (not part of a bound region). These indices can be used to form a BED file, see example below.

## Author(s)

Raphael Gottardo, [email protected]

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24``` ```# Load the data data(ER) # Only select the first 5000 probes for speed-up ER<-ER[1:5000,] # Calculate the joint posterior probabilities #Only use 100 iterations for speed up (You should use more! See default value) BAConER<-BAC(ER[,5:7], ER[,2:4], B=100,verbose=FALSE,w=5) # For Regions using 0.5 cut-off for the joint posterior probabilities ERregions<-CallRegions(ER[,1],BAConER\$jointPP,cutoff=0.5,maxGap=500) # Create the BED file nRegions<-max(ERregions) BED<-matrix(0,nRegions,4) for(i in 1:nRegions) { BED[i,2:3]<-range(ER[ERregions==i,1]) #The score should be between 0 and 1000 BED[i,4]<-max(BAConER\$jointPP[ERregions==i])*1000 } BED<-data.frame(BED) # The ER data is a subset of chr 21 BED[,1]<-"chr21" names(BED)<-c("chrom","chromStart","chromEnd","Score") # print it print(BED) ```