test_geneSet {FindIT2} | R Documentation

## test_geneSet

### Description

test_geneSet

### Usage

    data(test_geneSet)

### Format

character vector represent your interesting gene set

### Examples

    ## Not run:
    # source
    if (require(TxDb.Athaliana.BioMart.plantsmart28)) {
        library(FindIT2)
        Txdb <- TxDb.Athaliana.BioMart.plantsmart28
        seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C"))
        ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
        ChIP_peak_GR <- loadPeakFile(ChIP_peak_path)
        ATAC_peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
        ATAC_peak_GR <- loadPeakFile(ATAC_peak_path)

        mmAnno_geneScan <- mm_geneScan(
            peak_GR = ChIP_peak_GR,
            Txdb = Txdb,
            upstream = 2e4,
            downstream = 2e4
        )

        peakRP_gene <- calcRP_TFHit(
            mmAnno = mmAnno_geneScan,
            Txdb = Txdb,
            report_fullInfo = FALSE
        )

        data("RNADiff_LEC2_GR")
         merge_result <- integrate_ChIP_RNA(
            result_geneRP = peakRP_gene,
            result_geneDiff = RNADiff_LEC2_GR
        )

        target_result <- merge_result$data
        test_geneSet <- target_result$gene_id[1:50]

        related_peaks <- mm_geneBound(
            peak_GR = ATAC_peak_GR,
            Txdb = Txdb,
            input_genes = test_geneSet
        )
        test_featureSet <- unique(related_peaks$feature_id)
        # save(test_geneSet, file = "data/test_geneSet.rda", version = 2)
        # save(test_featureSet, file = "data/test_featureSet.rda", version = 2)
    }

    ## End(Not run)

[Package FindIT2 version 1.0.3 Index]