calcRP_region: calcRP_region

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

calcRP_region

Description

calculate regulatory potential based on mm_geneScan result and peakCount matrix, which is useful for ATAC or H3K27ac histone modification data.

Usage

calcRP_region(
  mmAnno,
  peakScoreMt,
  Txdb,
  Chrs_included,
  decay_dist = 1000,
  log_transform = FALSE,
  verbose = TRUE
)

Arguments

mmAnno	the annotated GRange object from mm_geneScan
peakScoreMt	peak count matrix. The rownames are feature_id in mmAnno, while the colnames are sample names
Txdb	Txdb
Chrs_included	a character vector which represent chromosome where you want to calculate gene RP in. If Chromosome is not be set, it will calculate gene RP in all chromosomes in Txdb.
decay_dist	decay distance
log_transform	whether you want to log and norm your RP
verbose	whether you want to report detailed running message

Value

a MultiAssayExperiment object containg detailed peak-RP-gene relationship and sumRP info

Examples

if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
    data("ATAC_normCount")
    library(SummarizedExperiment)
    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)
    mmAnno <- mm_geneScan(peak_GR, Txdb)

    regionRP <- calcRP_region(
        mmAnno = mmAnno,
        peakScoreMt = ATAC_normCount,
        Txdb = Txdb,
        Chrs_included = "Chr5"
    )

    sumRP <- assays(regionRP)$sumRP
    fullRP <- assays(regionRP)$fullRP
}

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