test_geneSet {FindIT2} | R Documentation |
test_geneSet
data(test_geneSet)
character vector represent your interesting gene set
## 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)