scan_motifs {spatzie} | R Documentation |
Uses motifmatchR to scan interaction regions for given motifs.
scan_motifs(int_data, motifs, genome)
int_data |
a |
motifs |
a TFBS tools matrix of DNA binding motifs |
genome |
BSgenome object or DNAStringSet object, must match chromosomes from interaction data file |
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
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) ## 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)