WindowSizeRecog: WindowSizeRecog is a function to specify window size for each...

In CREAM: Clustering of Genomic Regions Analysis Method

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

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)

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