WindowVec: WindowVec is a function to specify window size for each order...

In CREAM: Clustering of Genomic Regions Analysis Method

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)

CREAM documentation built on May 2, 2019, 6:57 a.m.