kmax {spiky} | R Documentation |
simple contig kmer comparisons
kmax(km, normalize = TRUE)
km |
kmer summary |
normalize |
normalize (divide by row sums)? (TRUE) |
the most common kmers for each contig, across all contigs
data(genbank_mito, package="spiky") mtk6 <- kmers(genbank_mito, k=6) rownames(mtk6) <- paste0(rownames(mtk6), "_MT") kmax(mtk6) data(phage, package="spiky") phk6 <- kmers(phage, k=6) kmax(phk6, normalize=FALSE) stopifnot(identical(colnames(phk6), colnames(mtk6))) k6 <- rbind(mtk6, phk6) kmax(k6) library(BSgenome.Mmusculus.UCSC.mm10.masked) mm10k6 <- kmers(Mmusculus) rownames(mm10k6) <- paste0("mm10_", rownames(mm10k6)) library(BSgenome.Hsapiens.UCSC.hg38.masked) hg38k6 <- kmers(Hsapiens) rownames(hg38k6) <- paste0("hg38_", rownames(hg38k6)) hgmmphmtk6 <- rbind(hg38k6[paste0("hg38_chr", 1:22), ], mm10k6[paste0("mm10_chr", 1:19), ], phk6, mtk6) Heatmap(kmax(hgmmphmtk6), name="Pr(kmer)")