get_specific_interactions: Get interactions that contain a specific motif pair

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

Get interactions that contain a specific motif pair

Description

Select interactions that contain anchor1_motif within anchor 1 and anchor2_motif within anchor 2.

Usage

get_specific_interactions(
  interaction_data,
  anchor1_motif = NULL,
  anchor2_motif = NULL
)

Arguments

interaction_data	an interactionData object of paired genomic regions
anchor1_motif	Motif name from interactionData$anchor1_motifs
anchor2_motif	Motif name from interactionData$anchor2_motifs

Value

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

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)
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")

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