TFsEnrichInRegions {enrichTF} | R Documentation |
Test each TF is enriched in regions or not
enrichTFsEnrichInRegions(enrichStep, inputRegionBed = NULL, inputForegroundGeneBed = NULL, inputBackgroundGeneBed = NULL, inputRegionMotifBed = NULL, outputTFsEnrichTxt = NULL, inputMotifWeights = NULL, inputTFgeneRelMtx = NULL, inputMotifTFTable = NULL, ...) ## S4 method for signature 'Step' enrichTFsEnrichInRegions(enrichStep, inputRegionBed = NULL, inputForegroundGeneBed = NULL, inputBackgroundGeneBed = NULL, inputRegionMotifBed = NULL, outputTFsEnrichTxt = NULL, inputMotifWeights = NULL, inputTFgeneRelMtx = NULL, inputMotifTFTable = NULL, ...) tfsEnrichInRegions(inputRegionBed, inputForegroundGeneBed, inputBackgroundGeneBed, inputRegionMotifBed, outputTFsEnrichTxt = NULL, inputMotifWeights = NULL, inputTFgeneRelMtx = NULL, inputMotifTFTable = NULL, ...)
enrichStep |
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inputRegionBed |
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inputForegroundGeneBed |
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inputBackgroundGeneBed |
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inputRegionMotifBed |
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outputTFsEnrichTxt |
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inputMotifWeights |
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inputTFgeneRelMtx |
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inputMotifTFTable |
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... |
Additional arguments, currently unused. |
Connect foreground and background regions to targetGene. If you only use this function without previous steps and you do not familiar with the data format of the input, you can run the example to see the example input from previous steps.
An invisible EnrichStep-class
object
(Step-class
based) scalar for downstream analysis.
Zheng Wei
genBackground
findMotifsInRegions
tfsEnrichInRegions
library(magrittr) setGenome("testgenome") #Use "hg19","hg38",etc. for your application foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed") gen <- genBackground(inputForegroundBed = foregroundBedPath) conTG <- enrichRegionConnectTargetGene(gen) findMotif <- enrichFindMotifsInRegions(gen,motifRc="integrate") result <- enrichTFsEnrichInRegions(gen) genBackground(inputForegroundBed = foregroundBedPath) %>% enrichRegionConnectTargetGene %>% enrichFindMotifsInRegions(motifRc="integrate") %>% enrichTFsEnrichInRegions