integrate_ChIP_RNA {FindIT2} | R Documentation |
integrate ChIP-Seq and RNA-Seq data to find TF target genes
integrate_ChIP_RNA( result_geneRP, result_geneDiff, lfc_threshold = 1, padj_threshold = 0.05 )
result_geneRP |
the simplify result from calcRP_TFHit(report_fullInfo = FALSE) or RP_df <- metadata(fullRP_hit)$peakRP_gene. |
result_geneDiff |
the result from RNA diff result with three column gene_id, log2FoldChange, padj |
lfc_threshold |
the threshold which decide significant genes |
padj_threshold |
the threshold which decide significant genes |
a ggplot object if having significant genes in your result. If not, it will report a data.frame with integrated info.
if (require(TxDb.Athaliana.BioMart.plantsmart28)) { data("RNADiff_LEC2_GR") Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2") peak_GR <- loadPeakFile(peak_path) mmAnno <- mm_geneScan(peak_GR, Txdb) result_geneRP <- calcRP_TFHit( mmAnno = mmAnno, Txdb = Txdb ) # output a plot merge_data <- integrate_ChIP_RNA( result_geneRP = result_geneRP, result_geneDiff = RNADiff_LEC2_GR ) # if you want to extract merge target data target_data <- merge_data$data }