Description Usage Arguments Value Author(s) Examples
Function searches the CREs for given TFs in region.
1 2 | TFBSsOnChromosome(arrayData = "", nameChromosome = "chr21", begin = "", end = "",
firstCut = "in", secondCut = "in", massTF = 10000, powerNR = 20)
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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. |
Data Frame (class = "data.frame") of set of CREs.
Alexey Solovyev
1 2 3 4 5 | 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)
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