matchKmers: matchKmers

In GreenleafLab/chromVAR: Chromatin Variation Across Regions

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)

GreenleafLab/chromVAR documentation built on Aug. 20, 2019, 11:39 a.m.