library(SVAlignR) data(longreads) seqs <- longreads$connection[1:15] pad <- c(rep("0", 9), rep("", 6)) names(seqs) <- paste("LR", pad, 1:length(seqs), sep = "") seqs <- seqs[!duplicated(seqs)] alfa <- Cipher(seqs) seqclust <- SequenceCluster(seqs, NC = 5) plot(seqclust) coded <- encode(alfa, seqclust@rawSequences) kmers <- lapply(1:11, function(N) {countWords(coded, N)}) #motifNodes <- lapply(kmers, function(x) x[names(x) %in% names(motifs)]) #save(alfa, motifs, kmers, motifNodes, decomp, # file = file.path(paths$scratch, "motifNodes.Rda"))