PeakMinFilt

Table of indetified COREs before filteration

Clusters_init

Vector of window sizes ordered based on order of CORE

WindowVecFinal

PeakMinFilt is a function to filter the lowest Order of COREs which distance
between functional regions is close to the corresponding Window Size

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.

Benjamin HaibeKains

CREAM

Clustering of Genomic Regions Analysis Method

Seyed Ali Madani Tonekaboni

Victor Kofia

Mathieu Lupien

Benjamin Haibe-Kains

PeakMinFilt function

PeakMinFilt is a function to filter the lowest Order of COREs which distance
between functional regions is close to the corresponding Window Size — PeakMinFilt

PeakMinFilt: PeakMinFilt is a function to filter the lowest Order of COREs which distance between functional regions is close to the corresponding Window Size

Description

Usage

Arguments

Value