| Type: | Package |
| Title: | Clustering of Genomic Regions Analysis Method |
| Version: | 1.1.1 |
| Date: | 2018-05-30 |
| Description: | Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach. |
| License: | GPL (≥ 3) |
| Imports: | stats, utils |
| Depends: | R (≥ 3.3) |
| URL: | https://github.com/bhklab/CREAM |
| Suggests: | testthat |
| RoxygenNote: | 6.0.1 |
| LazyData: | true |
| biocViews: | PeakDetection, FunctionalPrediction, BiomedicalInformatics, Clustering |
| BugReports: | https://github.com/bhklab/CREAM/issues |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2018-06-04 13:45:12 UTC; root |
| Author: | Seyed Ali Madani Tonekaboni [aut], Victor Kofia [aut], Mathieu Lupien [aut], Benjamin Haibe-Kains [aut, cre] |
| Maintainer: | Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca> |
| Repository: | CRAN |
| Date/Publication: | 2018-06-06 09:07:56 UTC |
CREAM is the main function for CORE identification
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)
ElementRecog is a function to identify COREs
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)
PeakMinFilt is a function to filter the lowest Order of COREs which distance between functional regions is close to the corresponding Window Size
Description
PeakMinFilt is a function to filter the lowest Order of COREs which distance between functional regions is close to the corresponding Window Size
Usage
PeakMinFilt(Clusters_init, WindowVecFinal)
Arguments
Clusters_init |
Table of indetified COREs before filteration |
WindowVecFinal |
Vector of window sizes ordered based on order of CORE |
Value
Minimum order of COREs
WindowSizeRecog is a function to specify window size for each order of COREs
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)
WindowVec is a function to specify window size for each order of COREs
Description
WindowVec is a function to specify window size for each order of COREs
Usage
WindowVec(InputData, peakNumMin, 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. |
peakNumMin |
Minimum order of COREs |
WScutoff |
Threshold used to identify WS within distribution of maximum distance between peaks for each order of CORE |
Value
Vector of window sizes from order 2 up to maximum order of COREs
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)