matchMotifs: matchMotifs

In motifmatchr: Fast Motif Matching in R

Description

Find motif matches

Usage

matchMotifs(pwms, subject, ...)

## S4 method for signature 'PWMatrixList,DNAStringSet'
matchMotifs(pwms, subject,
  genome = NULL, bg = c("subject", "genome", "even"), out = c("matches",
  "scores", "positions"), p.cutoff = 5e-05, w = 7, ranges = NULL)

## S4 method for signature 'PWMatrixList,character'
matchMotifs(pwms, subject, genome = NULL,
  bg = c("subject", "genome", "even"), out = c("matches", "scores",
  "positions"), p.cutoff = 5e-05, w = 7, ranges = NULL)

## S4 method for signature 'PWMatrixList,DNAString'
matchMotifs(pwms, subject, genome = NULL,
  bg = c("subject", "genome", "even"), out = c("matches", "scores",
  "positions"), p.cutoff = 5e-05, w = 7, ranges = NULL)

## S4 method for signature 'PWMatrixList,GenomicRanges'
matchMotifs(pwms, subject,
  genome = GenomeInfoDb::genome(subject), bg = c("subject", "genome",
  "even"), out = c("matches", "scores", "positions"), p.cutoff = 5e-05,
  w = 7)

## S4 method for signature 'PWMatrixList,RangedSummarizedExperiment'
matchMotifs(pwms, subject,
  genome = GenomeInfoDb::genome(subject), bg = c("subject", "genome",
  "even"), out = c("matches", "scores", "positions"), p.cutoff = 5e-05,
  w = 7)

## S4 method for signature 'PWMatrixList,BSgenomeViews'
matchMotifs(pwms, subject,
  bg = c("subject", "genome", "even"), out = c("matches", "scores",
  "positions"), p.cutoff = 5e-05, w = 7)

## S4 method for signature 'PFMatrixList,ANY'
matchMotifs(pwms, subject, ...)

## S4 method for signature 'PWMatrix,ANY'
matchMotifs(pwms, subject, ...)

## S4 method for signature 'PFMatrix,ANY'
matchMotifs(pwms, subject, ...)

Arguments

pwms	either PFMatrix, PFMatrixList, PWMatrix, PWMatrixList
subject	either GenomicRanges, DNAStringSet, DNAString, or character vector
...	additional arguments depending on inputs
genome	BSgenome object, DNAStringSet, or FaFile, or short string signifying genome build recognized by getBSgenome. Only required if subject is GenomicRanges or RangedSummarizedExperiment or if bg is set to "genome"
bg	background nucleotide frequencies. Default is to compute based on subject, i.e. the specific set of sequences being evaluated. See Details.
out	what to return? see return section
p.cutoff	p-value cutoff for returning motifs
w	parameter controlling size of window for filtration; default is 7
ranges	if subject is not GenomicRanges or RangedSummarizedExperiment, these ranges can be used to specify what ranges the input sequences correspond to. These ranges will be incorporated into the SummarizedExperiment output if out is "matches" or "scores" or will be used to give absolute positions of motifs if out is "positions"

Details

Background nucleotide frequencies can be set to "subject" to use the subject sequences or ranges for computing the nucleotide frequencies, "genome" for using the genomice frequencies (in which case a genome must be specified), "even" for using 0.25 for each base, or a numeric vector with A, C, G, and T frequencies.

Value

Either returns a SummarizedExperiment with a sparse matrix with values set to TRUE for a match (if out == 'matches'), a SummarizedExperiment with a matches matrix as well as matrices with the maximum motif score and total motif counts (if out == 'scores'), or a GenomicRangesList or a list of IRangesList with all the positions of matches (if out == 'positions')

Methods (by class)

• pwms = PWMatrixList,subject = DNAStringSet: PWMatrixList/DNAStringSet

• pwms = PWMatrixList,subject = character: PWMatrixList/character

• pwms = PWMatrixList,subject = DNAString: PWMatrixList/DNAString

• pwms = PWMatrixList,subject = GenomicRanges: PWMatrixList/GenomicRanges

• pwms = PWMatrixList,subject = RangedSummarizedExperiment: PWMatrixList/RangedSummarizedExperiment

• pwms = PWMatrixList,subject = BSgenomeViews: PWMatrixList/BSGenomeViews

• pwms = PFMatrixList,subject = ANY: PFMatrixList/ANY

• pwms = PWMatrix,subject = ANY: PWMatrix/ANY

• pwms = PFMatrix,subject = ANY: PFMatrix/ANY

Examples

data(example_motifs, package = "motifmatchr")

# Make a set of peaks
peaks <- GenomicRanges::GRanges(seqnames = c("chr1","chr2","chr2"),
                ranges = IRanges::IRanges(start = c(76585873,42772928,
                                          100183786),
                                          width = 500))

# Get motif matches for example motifs
motif_ix <- matchMotifs(example_motifs, peaks, genome = "BSgenome.Hsapiens.UCSC.hg19")

motifmatchr documentation built on Nov. 8, 2020, 8:09 p.m.