fractionCellTF: Fraction of factors of the dominating cellular line

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

Fraction of factors of the dominating cellular line

Description

Function counts fraction of factors of the dominating cellular line.

Usage

fractionCellTF(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 50, powerNR = 3, limitPart = 0.2)

Arguments

arrayData	Data or path to data, by default "~/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	List of TFs or quantity of MACS-peaks to choose CRE.
powerNR	Minimal needed quantity of MACS-peaks to choose CRE.
limitPart	Minimal needed fraction of TFs.

Value

Data Frame (class = "data.frame") of CREs, dominante cellular line, quantity of type of cellular lines, quantity of different TFs, quantity of TFs of dominating cellular line and fraction of TFs of dominating cellular line.

Author(s)

Alexey Solovyev

Examples

myFrame <- fractionCellTF(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 50, powerNR = 3, limitPart = 0.2)

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