motifKmerSimilarity {monaLisa} | R Documentation |
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).
motifKmerSimilarity( x, kmerLen = 5, kmers = NULL, includeRevComp = FALSE, BPPARAM = SerialParam(), verbose = FALSE )
x |
Either a |
kmerLen |
A |
kmers |
Either a character vector of k-mers for which to calculate
the similarity to each motif, or |
includeRevComp |
A |
BPPARAM |
An optional |
verbose |
A logical scalar. If |
A matrix of probabilties for each motif - k-mer pair.
bplapply
used for parallelization.
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")]