findIT_TFHit {FindIT2} | R Documentation |
find influential TF of your input gene set based on TF ChIP-Seq or motif data
findIT_TFHit( input_genes, Txdb, TF_GR_database, scan_dist = 20000, decay_dist = 1000, Chrs_included, background_genes = NULL, background_number = 3000, verbose = TRUE )
input_genes |
a character vector which represent genes set which you want to find influential TF for |
Txdb |
Txdb |
TF_GR_database |
TF peak GRange with a column named TF_id representing you TF name |
scan_dist |
scan distance |
decay_dist |
decay distance |
Chrs_included |
a character vector represent chromosomes which you want to sample background genes from |
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 |
data.frame
if (require(TxDb.Athaliana.BioMart.plantsmart28)) { data("test_geneSet") 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) ChIP_peak_GR$TF_id <- "AT1G28300" set.seed(20160806) result_findIT_TFHit <- findIT_TFHit( input_genes = test_geneSet, Txdb = Txdb, TF_GR_database = ChIP_peak_GR ) }