WindowVec {CREAM}

WindowVec is a function to specify window size for each order of COREs

Description

WindowVec is a function to specify window size for each order of COREs

Usage

WindowVec(InputData, peakNumMin, WScutoff)

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.

peakNumMin

Minimum order of COREs

WScutoff

Threshold used to identify WS within distribution of maximum distance between peaks for each order of CORE

Value

Vector of window sizes from order 2 up to maximum order of COREs

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)