findIT_regionRP {FindIT2} | R Documentation |
find Influential TF of your input gene set based on regulatory potential data and TF ChIP-Seq or motif data
findIT_regionRP( regionRP, Txdb, TF_GR_database, input_genes, background_genes = NULL, background_number = 3000, verbose = TRUE )
regionRP |
the MultiAssayExperiment object from calcRP_region |
Txdb |
Txdb |
TF_GR_database |
TF peak GRange with a column named TF_id representing you TF name |
input_genes |
a character vector which represent genes set which you want to find influential TF for |
background_genes |
a character vector which represent background genes set. If you do not assign background gene , program will sample background_number genes as background genes from all gene sets. |
background_number |
background genes number |
verbose |
whether you want to report detailed running message |
a MultiAssayExperiment object containg detailed TF-percent and TF-pvalue
if (require(TxDb.Athaliana.BioMart.plantsmart28)) { data("ATAC_normCount") data("test_geneSet") Txdb <- TxDb.Athaliana.BioMart.plantsmart28 seqlevels(Txdb) <- paste0("Chr", c(1:5, "M", "C")) peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2") peak_GR <- loadPeakFile(peak_path) ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2") ChIP_peak_GR <- loadPeakFile(ChIP_peak_path) ChIP_peak_GR$TF_id <- "AT1G28300" mmAnno <- mm_geneScan(peak_GR, Txdb) regionRP <- calcRP_region( mmAnno = mmAnno, peakScoreMt = ATAC_normCount, Txdb = Txdb, Chrs_included = "Chr5" ) set.seed(20160806) result_findIT_regionRP <- findIT_regionRP( regionRP = regionRP, Txdb = Txdb, TF_GR_database = ChIP_peak_GR, input_genes = test_geneSet, background_number = 3000 ) }