integrate_ChIP_RNA {FindIT2} | R Documentation

## integrate_ChIP_RNA

### Description

integrate ChIP-Seq and RNA-Seq data to find TF target genes

### Usage

    integrate_ChIP_RNA(
      result_geneRP,
      result_geneDiff,
      lfc_threshold = 1,
      padj_threshold = 0.05
    )

### Arguments

`result_geneRP` | the simplify result from calcRP_TFHit(report_fullInfo = FALSE) or RP_df <- metadata(fullRP_hit)$peakRP_gene.
`result_geneDiff` | the result from RNA diff result with three column gene_id, log2FoldChange, padj
`lfc_threshold` | the threshold which decide significant genes
`padj_threshold` | the threshold which decide significant genes

### Value

a ggplot object if having significant genes in your result. If not, it will report a data.frame with integrated info.

### Examples

    if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
        data("RNADiff_LEC2_GR")
        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)

        result_geneRP <- calcRP_TFHit(
            mmAnno = mmAnno,
            Txdb = Txdb
        )
        # output a plot
        merge_data <- integrate_ChIP_RNA(
            result_geneRP = result_geneRP,
            result_geneDiff = RNADiff_LEC2_GR
        )
        # if you want to extract merge target data
        target_data <- merge_data$data

    }

[Package FindIT2 version 1.0.3 Index]