## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE,warning = FALSE) ## ----installpkg,eval=FALSE,message=FALSE,warning=FALSE------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("enrichTF") ## ----loading00,eval=TRUE,message=FALSE---------------------------------------- library(enrichTF) ## ----eval=TRUE---------------------------------------------------------------- # Provide your region list in BED format with 3 columns. foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed") # Call the whole pipeline PECA_TF_enrich(inputForegroundBed = foregroundBedPath, genome = "testgenome") # change"testgenome" to one of "hg19", "hg38", "mm9", 'mm10' ! "testgenome" is only a test example. ## ----------------------------------------------------------------------------- printMap() ## ----loading01---------------------------------------------------------------- setGenome("testgenome") foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed") gen <- genBackground(inputForegroundBed = foregroundBedPath) ## ----loading02---------------------------------------------------------------- conTG <- enrichRegionConnectTargetGene(gen) ## ----loading03---------------------------------------------------------------- findMotif <- enrichFindMotifsInRegions(gen,motifRc="integrate") ## ----eval=TRUE---------------------------------------------------------------- result <- enrichTFsEnrichInRegions(gen) ## ----------------------------------------------------------------------------- library(magrittr) setGenome("testgenome") foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed") result <- genBackground(inputForegroundBed = foregroundBedPath) %>% enrichRegionConnectTargetGene%>% enrichFindMotifsInRegions(motifRc="integrate") %>% enrichTFsEnrichInRegions ## ----------------------------------------------------------------------------- examplefile <- system.file(package = "enrichTF", "extdata","result.example.txt") read.table(examplefile, sep='\t', header = TRUE)%>% knitr::kable() ## ----------------------------------------------------------------------------- sessionInfo()