scan_motifs: Scans interaction file for motif instances

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

Scans interaction file for motif instances

Description

Uses motifmatchR to scan interaction regions for given motifs.

Usage

scan_motifs(int_data, motifs, genome)

Arguments

int_data	a GenomicInteractions object of paired genomic regions
motifs	a TFBS tools matrix of DNA binding motifs
genome	BSgenome object or DNAStringSet object, must match chromosomes from interaction data file

Value

an interaction data object where obj$anchor1_motifs and obj$anchor2_motifs contain information about the scores and matches to motifs from anchor one and anchor two of interaction data genomic regions

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)

## End(Not run)

motifs_file <- system.file("extdata/motifs_subset.txt.gz",
                           package = "spatzie")
motifs <- TFBSTools::readJASPARMatrix(motifs_file, matrixClass = "PFM")
left <- GenomicRanges::GRanges(
  seqnames = c("chr1", "chr1", "chr1"),
  ranges = IRanges::IRanges(start = c(1, 15, 20),
                            end = c(10, 35, 31)))
right <- GenomicRanges::GRanges(
  seqnames = c("chr1", "chr2", "chr2"),
  ranges = IRanges::IRanges(start = c(17, 47, 41),
                            end = c(28, 54, 53)))
test_interactions <- GenomicInteractions::GenomicInteractions(left, right)

# toy DNAStringSet to replace BSgenome object
seqs <- c("chr1" = "CCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCC",
          "chr2" = "CTACAAACTAGGAATTTAGGCAAACCTGTGTTAAAATCTTAGCTCATTCATTAAT")
toy_genome <- Biostrings::DNAStringSet(seqs, use.names = TRUE)

res <- scan_motifs(test_interactions, motifs, toy_genome)

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