## ----message = FALSE---------------------------------------------------------- library(motifmatchr) library(GenomicRanges) library(SummarizedExperiment) library(BSgenome) # load some example motifs data(example_motifs, package = "motifmatchr") # Make a set of peaks peaks <- GRanges(seqnames = c("chr1","chr2","chr2"), ranges = IRanges(start = c(76585873,42772928,100183786), width = 500)) # Get motif matches for example motifs in peaks motif_ix <- matchMotifs(example_motifs, peaks, genome = "hg19") motifMatches(motif_ix) # Extract matches matrix from result # Get motif positions within peaks for example motifs in peaks motif_pos <- matchMotifs(example_motifs, peaks, genome = "hg19", out = "positions") ## ----------------------------------------------------------------------------- # using peaks motif_ix_peaks <- matchMotifs(example_motifs, peaks, genome = "hg19") # using SummarizedExperiment example_SummarizedExperiment <- SummarizedExperiment(assays = list(counts = matrix(1, ncol = 4, nrow = 3)), rowRanges = peaks) motif_ix_SummarizedExperiment <- matchMotifs(example_motifs, example_SummarizedExperiment, genome = "hg19") all.equal(motifMatches(motif_ix_peaks), motifMatches(motif_ix_SummarizedExperiment)) ## ----message = FALSE---------------------------------------------------------- # using BSgenomeViews example_BSgenomeViews <- BSgenomeViews(BSgenome.Hsapiens.UCSC.hg19, peaks) motif_ix_BSgenomeViews <- matchMotifs(example_motifs, example_BSgenomeViews) all.equal(motifMatches(motif_ix_peaks), motifMatches(motif_ix_BSgenomeViews)) ## ----message = FALSE---------------------------------------------------------- # using DNAStringSet library(Biostrings) library(BSgenome.Hsapiens.UCSC.hg19) example_DNAStringSet <- getSeq(BSgenome.Hsapiens.UCSC.hg19, peaks) motif_ix_DNAStringSet <- matchMotifs(example_motifs, example_DNAStringSet) all.equal(motifMatches(motif_ix_peaks), motifMatches(motif_ix_DNAStringSet)) ## ----message = FALSE---------------------------------------------------------- # using character vector example_character <- as.character(example_DNAStringSet) motif_ix_character <- matchMotifs(example_motifs, example_character) all.equal(motifMatches(motif_ix_peaks), motifMatches(motif_ix_character)) ## ----------------------------------------------------------------------------- motif_ix <- matchMotifs(example_motifs, peaks, genome = "hg19", bg = "even") ## ----------------------------------------------------------------------------- motif_ix <- matchMotifs(example_motifs, peaks, genome = "hg19", bg = "genome") ## ----------------------------------------------------------------------------- motif_ix <- matchMotifs(example_motifs, peaks, genome = "hg19", bg = c("A" = 0.2,"C" = 0.3, "G" = 0.3, "T" = 0.2)) ## ----message = FALSE---------------------------------------------------------- library(TFBSTools) example_pwms <- do.call(PWMatrixList,lapply(example_motifs, toPWM, pseudocounts = 0.5)) ## ----------------------------------------------------------------------------- motif_ix <- matchMotifs(example_motifs, peaks, genome = "hg19") print(motif_ix) head(motifMatches(motif_ix)) motif_ix_scores <- matchMotifs(example_motifs, peaks, genome = "hg19", out = "scores") print(motif_ix_scores) head(motifMatches(motif_ix_scores)) head(motifScores(motif_ix_scores)) head(motifCounts(motif_ix_scores)) motif_pos <- matchMotifs(example_motifs, peaks, genome = "hg19", out = "positions") print(motif_pos) ## ----------------------------------------------------------------------------- Sys.Date() ## ----------------------------------------------------------------------------- sessionInfo()