CREAM: CREAM is the main function for CORE identification

In CREAM: Clustering of Genomic Regions Analysis Method

Description

CREAM is the main function for CORE identification

Usage

CREAM(in_path, WScutoff = 1.5, MinLength = 1000, peakNumMin = 2)

Arguments

in_path	Path to the input file (The file inclusing the functional regions) Note. You have to make sure that there is no overlapping regions within the input file
WScutoff	Threshold used to identify WS within distribution of maximum distance between peaks for each order of CORE
MinLength	Criteria for the minimum number of functional regions in the input file
peakNumMin	Minimum number of peaks for CORE identification

Value

Bed file including the identified COREs

Examples

CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
MinLength = 1000, peakNumMin = 2)

Example output

[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
      [,1]    [,2]       [,3]      
 [1,] "chr21" "16424380" "16435150"
 [2,] "chr21" "36250900" "36261130"
 [3,] "chr21" "40166220" "40176750"
 [4,] "chr21" "44759600" "44764470"
 [5,] "chr21" "44829000" "44833330"
 [6,] "chr21" "44833600" "44836670"
 [7,] "chr21" "44837200" "44843050"
 [8,] "chr21" "44843340" "44848210"
 [9,] "chr21" "44910400" "44923490"
[10,] "chr21" "38737900" "38746590"
[11,] "chr21" "43178760" "43189030"
[12,] "chr21" "17565340" "17569790"
[13,] "chr21" "45183960" "45188350"

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