scan_motifs {spatzie} | R Documentation

## 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)

[Package spatzie version 1.0.1 Index]