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
1 2 3 | array <- arrayIntersections(arrayData = "", nameChromosome = "chr21",
begin = "", end = "", firstCut = "in", secondCut = "in", massTF = 10000,
powerNR = 10, tableNormal = TRUE)
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