#!/usr/bin/env R
#
# This file is part of CCCA,
# http://github.com/alexjgriffith/CCCA/,
# and is Copyright (C) University of Ottawa, 2015. It is Licensed under
# the three-clause BSD License; see LICENSE.txt.
# Author : Alexander Griffith
# Contact: griffitaj@gmail.com
# this file is for temporary c-wrapping
# it is dependant on the inclusion of mulcal
#' region wrapper
#' #experimental
#'
regionWrapper<-function(temp,chroms){
width<-length(chroms)
buffer<-as.integer(rep(0,width))
outMatrix<-integer((width+2)*(length-1))
length<-length(temp[,1])
.C("region",temp[,1],temp[,3],temp[,2],buffer,outMatrix,length,width)
}
#' peak Regions
#' #experimental
#'
peakRegions<-function(data){
chroms<-levels(data[,1])
subset<-data[,data[,1]==chroms[1]]
temp<-rbind(cbind(subset[,2],subset[,"name"],0),
cbind(subset[,3],subset[,"name"],1))
regionWrapper(temp,chroms)
}
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