peakGeneCor: peakGeneCor

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

peakGeneCor

Description

peakGeneCor

Usage

peakGeneCor(mmAnno, peakScoreMt, geneScoreMt, parallel = FALSE, verbose = TRUE)

Arguments

mmAnno	the annotated GRange object from mm_geneScan or mm_nearestGene
peakScoreMt	peak count matrix. The rownames are feature_id in mmAnno, while the colnames are sample names.
geneScoreMt	gene count matirx. The rownames are gene_id in mmAnno, while the colnames are sample names.
parallel	whehter you want to using bplapply to speed up calculation
verbose	whether you want to report detailed running message

Value

mmAnno with Cor, pvalue,padj,qvalue column

Examples

if (require(TxDb.Athaliana.BioMart.plantsmart28)){
    Txdb <- TxDb.Athaliana.BioMart.plantsmart28
    seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
    data("RNA_normCount")
    data("ATAC_normCount")
    peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
    peak_GR <- loadPeakFile(peak_path)[1:100]
    mmAnno <- mm_geneScan(peak_GR, Txdb)

    ATAC_colData <- data.frame(
        row.names = colnames(ATAC_normCount),
        type = gsub("_R[0-9]", "", colnames(ATAC_normCount))
    )

    ATAC_normCount_merge <- integrate_replicates(ATAC_normCount, ATAC_colData)
    RNA_colData <- data.frame(
        row.names = colnames(RNA_normCount),
        type = gsub("_R[0-9]", "", colnames(RNA_normCount))
    )
    RNA_normCount_merge <- integrate_replicates(RNA_normCount, RNA_colData)
    mmAnnoCor <- peakGeneCor(
        mmAnno = mmAnno,
        peakScoreMt = ATAC_normCount_merge,
        geneScoreMt = RNA_normCount_merge,
        parallel = FALSE
    )

    mmAnnoCor

}

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