peakGeneCor {FindIT2} | R Documentation

## 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

    }

[Package FindIT2 version 1.0.3 Index]