getAssocPairNumber: getAssocPairNumber

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

getAssocPairNumber

Description

get associated peak number of gene and vice verse.

Usage

getAssocPairNumber(
  mmAnno,
  output_type = c("gene_id", "feature_id"),
  output_summary = FALSE
)

Arguments

mmAnno	the annotated GRange object from mm_geneScan or mm_nearestGene
output_type	one of 'gene_id' or 'feature_id'
output_summary	whether you want to detailed info

Value

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)
    peakAnno <- mm_nearestGene(peak_GR, Txdb)

    getAssocPairNumber(peakAnno)

}

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