calcRP_TFHit: calcRP_TFHit

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

calcRP_TFHit

Description

calculate regulatory potential based on ChIP-Seq peak data, which is useful for TF ChIP-seq data.

Usage

calcRP_TFHit(
  mmAnno,
  Txdb,
  decay_dist = 1000,
  report_fullInfo = FALSE,
  verbose = TRUE
)

Arguments

mmAnno	the annotated GRange object from mm_geneScan
Txdb	Txdb
decay_dist	decay distance
report_fullInfo	whether you want to report full peak-RP-gene info
verbose	whether you want to report detailed running message

Details

If your origin peak_GR of mmAnno have column named feature_score, calcRP_TFHit will consider this column when calculating sumRP. Otherwise, it will consider all peak Hit feature_score is 1.

Value

if report_fullInfo is TRUE, it will output GRanges with detailed info. While FALSE, it will output data frame

Examples

if (require(TxDb.Athaliana.BioMart.plantsmart28)){
    Txdb <- TxDb.Athaliana.BioMart.plantsmart28
    seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
    peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
    peak_GR <- loadPeakFile(peak_path)
    mmAnno <- mm_geneScan(peak_GR, Txdb)

    # if you just want to get RP_df, you can set report_fullInfo FALSE
    fullRP_hit <- calcRP_TFHit(
        mmAnno = mmAnno,
        Txdb = Txdb,
        report_fullInfo = TRUE
    )

    RP_df <- metadata(fullRP_hit)$peakRP_gene

}

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