mm_geneScan: mm_geneScan

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

mm_geneScan

Description

Annotate peaks using geneScan mode, which means every peak have more than one related genes.

Usage

mm_geneScan(
  peak_GR,
  Txdb,
  upstream = 3000,
  downstream = 3000,
  reportGeneInfo = FALSE,
  verbose = TRUE,
  ...
)

Arguments

peak_GR	peak GRange with a column named feature_id representing you peak name
Txdb	Txdb
upstream	distance to start site(upstream)
downstream	distance to start site(downstream)
reportGeneInfo	whether you want to add gene info
verbose	whether you want to report detailed running message
...	additional arguments in findOverlaps

Value

Granges object with annotated info

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)
    peakAnno <- mm_geneScan(peak_GR, Txdb)
    peakAnno
}

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