filter_motifs {spatzie} | R Documentation |
Select a subset of motifs that are in at least a threshold fraction of regions. Motif subsets are selected separately for anchor one and anchor two regions.
filter_motifs(interaction_data, threshold)
interaction_data |
an interactionData object of paired genomic regions |
threshold |
fraction of interactions that should contain a motif for a motif to be considered |
an interactionData object where obj$anchor1_motif_indices
and obj$anchor2_motif_indices
have been filtered to motifs that are
present in a threshold fraction of interactions
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) ## End(Not run) res <- filter_motifs(spatzie::scan_interactions_example, threshold = 0.1)