TFBS: CREs for given TF

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

Description

Function searches the CREs for given TF in region.

Usage

TFBS(arrayData = "", nameChromosome = "chr21", begin = 5240000, end = 52450000,
firstCut = "in", secondCut = "in", TF = "AR", powerNR = 3)

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".
TF	Name of TF.
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

myFrame <- TFBS(arrayData = "", nameChromosome = "chr21", begin = 5240000, end = 52450000,
firstCut = "in", secondCut = "in", TF = "AR", powerNR = 3)

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