filter_motifs: Filter motifs based on occurrence within interaction data

In jhammelman/spatzie: Identification of enriched motif pairs from chromatin interaction data

Filter motifs based on occurrence within interaction data

Description

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.

Usage

filter_motifs(interaction_data, threshold)

Arguments

interaction_data	an interactionData object of paired genomic regions
threshold	fraction of interactions that should contain a motif for a motif to be considered

Value

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

Author(s)

Jennifer Hammelman

Examples

## 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)

jhammelman/spatzie documentation built on Feb. 8, 2024, 8:50 a.m.