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

In LosevAMU/remapR: Bioinformatic tools to transform ReMap-data in R

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.