ElementRecog {CREAM} | R Documentation |
ElementRecog is a function to identify COREs
ElementRecog(InputData, windowSize_Vec, peakNumMax, peakNumMin)
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) |
Identified COREs for the given input regions
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)