arrayIntersections: Counts array of intersections of Cis-regulatory elements...
In LosevAMU/remapR: Bioinformatic tools to transform ReMap-data in R

Description Usage Arguments Value Author(s) Examples

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

1 2	arrayIntersections(arrayData= "", nameChromosome = "chr21", begin = "", end = "", firstCut = "in", secondCut = "in", massTF = 30000, powerNR = 50, tableNormal = TRUE)

`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).

The square table of intersection of the CREs.

Alexey Solovyev

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