arrayIntersections: Counts array of intersections of Cis-regulatory elements...

View source: R/array_intersections.R

arrayIntersectionsR Documentation

Counts array of intersections of Cis-regulatory elements (CRE)

Description

For every TF the function counts how many other TFs can be found on CRE of given TF.

Usage

arrayIntersections(arrayData= "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 30000, powerNR = 50, tableNormal = TRUE)

Arguments

arrayData

Array of MACS-peaks in .bed or .RData format. Default folder is "~/tmp/RData/Output".

nameChromosome

Name of chromosome.

begin

Position of starting of searching on chromosome.

end

Position of ending of searching on chromosome.

firstCut

Can be "in" or "out". Condition of searching. "in" means that begin of MACS-peak can be before param "begin". "out" means that begin of MACS-peak can be only after param "begin".

secondCut

Can be "in" or "out". Condition of searching. "in" means that end of MACS-peak can be after param "end". "out" means that end of MACS-peak can be only before param "end".

massTF

can be number or list of TFs. Number means minimal quantity of presence of MACS-peaks in data, in other words the most frequent TFs.

powerNR

Hom many times TFs can be found in one location.

tableNormal

True or False. The way of presentation of the table: normalized (TRUE) or in the absolute values (FALSE).

Value

The square table of intersection of the CREs.

Author(s)

Alexey Solovyev

Examples

array <- arrayIntersections(arrayData = "", nameChromosome = "chr21",
begin = "", end = "", firstCut = "in", secondCut = "in", massTF = 10000,
powerNR = 10, tableNormal = TRUE)


LosevAMU/remapR documentation built on Sept. 25, 2024, 12:32 p.m.