kmax {spiky}

R Documentation

simple contig kmer comparisons

Description

simple contig kmer comparisons

Usage

kmax(km, normalize = TRUE)

Arguments

km	kmer summary
normalize	normalize (divide by row sums)? (TRUE)

Value

       the most common kmers for each contig, across all contigs

Examples

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)")

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