matchKmers {chromVAR} | R Documentation

## matchKmers

### Description

Find kmer matches in the DNA string-based subject

### Usage

    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, ...)

### Arguments

`k` | k
`subject` | either `GenomicRanges`, `DNAStringSet`, `DNAString`, or character vector
`...` | 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 `GenomicRanges`

### Details

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

### Value

SummarizedExperiment with matches assay storing which peaks contain which kmers

### Methods (by class)

- `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

### See Also

`getAnnotations`, `computeDeviations`

### Examples

    # 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)

[Package chromVAR version 1.8.0 Index]