CREAM (version 1.1.1)

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

Description

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

Usage

WindowSizeRecog(InputData, COREorder, 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.

COREorder

Order of the COREs which window size has to be determined for.

WScutoff

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

Value

Window size identified for each order of CORE

Examples

# NOT RUN {
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
WindowSize <- WindowSizeRecog(InputData, peakNumMin, WScutoff)
# }