test_geneSet: test_geneSet

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

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)

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