calcRP_coverage: calcRP_coverage

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

calcRP_coverage

Description

calculate regulatory potential using big wig files, which is useful for ATAC or H3K27ac histone modification data.

Usage

calcRP_coverage(
  bwFile,
  Txdb,
  gene_included,
  Chrs_included,
  decay_dist = 1000,
  scan_dist = 20000,
  verbose = TRUE
)

Arguments

bwFile	bw file
Txdb	Txdb
gene_included	a character vector which represent gene set which you want to calculate RP for
Chrs_included	a character vector which represent chromosomes where you want to calculate gene RP in
decay_dist	decay distance
scan_dist	scan distance
verbose	whether you want to report detailed running message

Details

Please note that because of rtracklayer::import has some issue on 32 bit R of windows, so the calcRP_coverage can not work on this system. But if your R is 64 bit, which now be applied on the most windows R, this function still work.

Value

data.frame

Examples

if (.Platform$OS.type != "windows" & require(TxDb.Athaliana.BioMart.plantsmart28)) {
    Txdb <- TxDb.Athaliana.BioMart.plantsmart28
    seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
    bwFile <- system.file("extdata", "E50h_sampleChr5.bw", package = "FindIT2")

    RP_df <- calcRP_coverage(
        bwFile = bwFile,
        Txdb = Txdb,
        Chrs_included = "Chr5"
    )

}

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