get_specific_interactions {spatzie} | R Documentation |
Select interactions that contain anchor1_motif within anchor 1 and anchor2_motif within anchor 2.
get_specific_interactions( interaction_data, anchor1_motif = NULL, anchor2_motif = NULL )
interaction_data |
an interactionData object of paired genomic regions |
anchor1_motif |
Motif name from |
anchor2_motif |
Motif name from |
a GenomicInteractions
object
containing a subset subset of interactions that contain an instance of
anchor1_motif
in anchor 1 and anchor2_motif
in anchor 2
Jennifer Hammelman
## Not run: genome_id <- "BSgenome.Mmusculus.UCSC.mm9" if (!(genome_id %in% rownames(utils::installed.packages()))) { BiocManager::install(genome_id, update = FALSE, ask = FALSE) } genome <- BSgenome::getBSgenome(genome_id) motifs_file <- system.file("extdata/motifs_subset.txt.gz", package = "spatzie") motifs <- TFBSTools::readJASPARMatrix(motifs_file, matrixClass = "PFM") yy1_pd_interaction <- scan_motifs(spatzie::interactions_yy1, motifs, genome) yy1_pd_interaction <- filter_motifs(yy1_pd_interaction, 0.4) yy1_pd_count_corr <- anchor_pair_enrich(yy1_pd_interaction, method = "score") yy1_yy1_interactions <- get_specific_interactions( yy1_pd_interaction, anchor1_motif = "YY1", anchor2_motif = "YY1") ## End(Not run) res <- get_specific_interactions(spatzie::int_data_yy1, anchor1_motif = "YY1", anchor2_motif = "YY1")