ElementRecog: ElementRecog is a function to identify COREs

In bhklab/CREAM: Clustering of Genomic Regions Analysis Method

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)

bhklab/CREAM documentation built on Feb. 16, 2021, 1:33 p.m.