Calculate similarities between motifs and k-mers.

For each motif, calculate it's similarity to all k-mers of length kmerLen, defined as the maximal probability of observing the k-mer given the base frequencies of the motif (the maximum is taken over for all possible ungapped alignments between motif and k-mer). If necessary matrices are padded on the sides with background base frequencies (assuming all bases to have a frequency of 0.25).

Usage

motifKmerSimilarity(
  x,
  kmerLen = 5,
  kmers = NULL,
  includeRevComp = FALSE,
  BPPARAM = SerialParam(),
  verbose = FALSE
)

Arguments

x

Either a PFMatrixList, or a character scalar with a file containing motifs in HOMER format (used directly method = "HOMER", loaded into a PFMatrixList by homerToPFMatrixList for method = "R").

kmerLen

A numeric scalar giving the k-mer length.

kmers

Either a character vector of k-mers for which to calculate the similarity to each motif, or NULL, in which case all k-mers of length kmerLen are used.

includeRevComp

A logical scalar. If set to TRUE, each k-mer as well as its reverse complement is compared to each motif, and the larger of the two similarities is returned.

BPPARAM

An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation.

verbose

A logical scalar. If TRUE, report on progress.

Value

A matrix of probabilties for each motif - k-mer pair.

See also

bplapply used for parallelization.

Examples

m <- rbind(A = c(12,  0,  0),
           C = c( 3,  2,  0),
           G = c( 0, 14,  0),
           T = c( 0,  0, 15))
pfms <- TFBSTools::PFMatrixList(
    TFBSTools::PFMatrix(name = "m1", profileMatrix = m),
    TFBSTools::PFMatrix(name = "m2", profileMatrix = m[, 3:1])
)
motifKmerSimilarity(pfms, kmerLen = 3)[, c("AGT", "TGA")]
#>       AGT    TGA
#> m1 0.7000 0.0625
#> m2 0.0625 0.7000