enhancerPromoterCor: enhancerPromoterCor

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

enhancerPromoterCor

Description

enhancerPromoterCor

Usage

enhancerPromoterCor(
  peak_GR,
  Txdb,
  up_scanPromoter = 500,
  down_scanPromoter = 500,
  up_scanEnhancer = 20000,
  down_scanEnhacner = 20000,
  peakScoreMt,
  parallel = FALSE,
  verbose = TRUE
)

Arguments

peak_GR	peak GRange with a column named feature_id representing you peak name
Txdb	Txdb
up_scanPromoter	the scan distance which is used to scan nearest promoter
down_scanPromoter	the scan distance which is used to scan nearest promoter
up_scanEnhancer	the scan distance which is used to scan feature
down_scanEnhacner	the scan distance which is used to scan feature
peakScoreMt	peak count matrix. The rownames are feature_id in peak_GR
parallel	whether you want to parallel to speed up
verbose	whether you want to report detailed running message

Value

mmAnno with Cor, pvalue,padj,qvalue column

Examples

if (require(TxDb.Athaliana.BioMart.plantsmart28)){
    data("ATAC_normCount")
    Txdb <- TxDb.Athaliana.BioMart.plantsmart28
    seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
    peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
    peak_GR <- loadPeakFile(peak_path)[1:100]
    mm_ePLink <- enhancerPromoterCor(
    peak_GR = peak_GR,
    Txdb = Txdb,
    peakScoreMt = ATAC_normCount,
    parallel = FALSE)
}

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.