ElementRecog {CREAM}

ElementRecog is a function to identify COREs

Description

ElementRecog is a function to identify COREs

Usage

ElementRecog(InputData, windowSize_Vec, peakNumMax, peakNumMin)

Arguments

InputData

The input data as a table including chromosome regions in which the first column is chromosome annotation, and second and third columns are start and ending positions.

windowSize_Vec

Vector of window sizes ordered based on order of CORE

peakNumMax

Maximum order of COREs (e.g. maximum number of peaks within COREs)

peakNumMin

Minimum order of COREs (e.g. minimum number of peaks within COREs)

Value

Identified COREs for the given input regions

Examples

InputData <- read.table(system.file("extdata", "A549_Chr21.bed",
package = "CREAM"), sep="\t")
colnames(InputData) <- c("chr", "start", "end")
MinLength <- 1000
if(nrow(InputData) < MinLength){
   stop(paste( "Number of functional regions is less than ", MinLength,
   ".", sep = "", collapse = ""))
}
peakNumMin <- 2
WScutoff <- 1.5
WindowVecFinal <- WindowVec(InputData, peakNumMin, WScutoff)
OutputList <- ElementRecog(InputData, WindowVecFinal,
(1+length(WindowVecFinal)), peakNumMin)