matchKmers {chromVAR} | R Documentation |
Find kmer matches in the DNA string-based subject
matchKmers(k, subject, ...) ## S4 method for signature 'character,DNAStringSet' matchKmers(k, subject, out = c("matches", "positions"), ranges = NULL) ## S4 method for signature 'character,character' matchKmers(k, subject, out = c("matches", "positions"), ranges = NULL) ## S4 method for signature 'character,DNAString' matchKmers(k, subject, out = c("matches", "positions"), ranges = NULL) ## S4 method for signature 'character,GenomicRanges' matchKmers(k, subject, genome = GenomeInfoDb::genome(subject), out = c("matches", "positions")) ## S4 method for signature 'character,RangedSummarizedExperiment' matchKmers(k, subject, ...) ## S4 method for signature 'numeric,ANY' matchKmers(k, subject, ...) ## S4 method for signature 'DNAStringSet,ANY' matchKmers(k, subject, ...) ## S4 method for signature 'DNAString,ANY' matchKmers(k, subject, ...)
k |
k |
subject |
either |
... |
additional arguments |
out |
what to return? see details |
ranges |
if subject is not GenomicRanges, ranges to use when out is positions |
genome |
BSgenome object, only used if subect is
|
Can either return a SummarizedExperiment with just sparse matrix with values set to 1 for a match (if return == 'matches'), or a GenomicRanges object with all the positions of matches
SummarizedExperiment with matches assay storing which peaks contain which kmers
k = character,subject = DNAStringSet
: For DNAStringSet Objects
k = character,subject = character
: For character strings
k = character,subject = DNAString
: For DNA String objects
k = character,subject = GenomicRanges
: For GenomicRanges
k = character,subject = RangedSummarizedExperiment
: For RangedSummarizedExperiment (containing GRanges in
rowRanges)
k = numeric,subject = ANY
: Catch-all for other un-documented types
k = DNAStringSet,subject = ANY
: Catch-all for other un-documented types with
DNAStringSet
k = DNAString,subject = ANY
: Catch-all for other un-documented types with DNAString
getAnnotations
, computeDeviations
# Load very small example counts (already filtered) data(mini_counts, package = "chromVAR") # Get peak-kmer annotation matrix for 6mers library(BSgenome.Hsapiens.UCSC.hg19) kmer_ix <- matchKmers(6, mini_counts, genome = BSgenome.Hsapiens.UCSC.hg19)