TFBSsOnChromosome: CREs for given list of TFs

Description Usage Arguments Value Author(s) Examples

Description

Function searches the CREs for given TFs in region.

Usage

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TFBSsOnChromosome(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 10000, powerNR = 20)

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.

Value

Data Frame (class = "data.frame") of set of CREs.

Author(s)

Alexey Solovyev

Examples

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myFrame <- TFBSsOnChromosome(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 10000, powerNR = 20)

myFrame <- TFBSsOnChromosome(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = c("AR", "FOXA1"), powerNR = 10)

LosevAMU/remapR documentation built on May 25, 2019, 12:23 p.m.