findIT_enrichWilcox {FindIT2} | R Documentation |
findIT_enrichWilcox
findIT_enrichWilcox( input_feature_id, peak_GR, TF_GR_database, background_peaks = NULL, background_number = 3000 )
input_feature_id |
a character vector which represent peaks set which you want to find influential TF for |
peak_GR |
a GRange object represent your whole feature location with a column named feature_id, which your input_feature_id should a part of it. |
TF_GR_database |
TF peak GRange with a column named TF_id representing you TF name |
background_peaks |
a character vector which represent background peak set. If you do not assign background peaks, program will sample background_number peaks as background peaks from all feature_id in your peak_GR |
background_number |
background peaks number |
data.frame
data("test_featureSet") 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" result_findIT_enrichWilcox <- findIT_enrichWilcox( input_feature_id = test_featureSet, peak_GR = peak_GR, TF_GR_database = ChIP_peak_GR )