jaccard_findIT_enrichFisher {FindIT2} | R Documentation |
jaccard_findIT_enrichFisher
jaccard_findIT_enrichFisher( input_feature_id, peak_GR, TF_GR_database, input_TF_id )
input_feature_id |
a character vector which represent peaks set which you want to find influential TF for (same as your find_IT_enrichFisher parameter) |
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 |
input_TF_id |
TF_id which you want to calculate jaccard index for |
jaccard similarity matrix
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$TF_id <- "AT1G28300" result_findIT_enrichFisher <- findIT_enrichFisher( input_feature_id = test_featureSet, peak_GR = peak_GR, TF_GR_database = ChIP_peak_GR ) jaccard_findIT_enrichFisher( input_feature_id = test_featureSet, peak_GR = peak_GR, TF_GR_database = ChIP_peak_GR, input_TF_id = result_findIT_enrichFisher$TF_id[1] )