WindowSizeRecog {CREAM} | R Documentation |
WindowSizeRecog is a function to specify window size for each order of COREs
WindowSizeRecog(InputData, COREorder, WScutoff)
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 |
Window size identified for each order of CORE
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)