Plot a histogram of kmer frequency across genes — kmer_hist • SeedMatchR

Plot a histogram of kmer frequency across genes

Usage

kmer_hist(
  seqs,
  target.seq,
  width = 7,
  step = 1,
  title = "K-mer gene frequencies"
)

Arguments

seqs: Input Biostrings::DNAStringSet
target.seq: Character vector of target seed sequence. Must be same size as width parameter.
width: Width of the kmer to count.
step: Step size for kmer window along the sequence.
title: Figure title

Value

A list of: *$plot: A histogram of frequencies X number of genes with kmer *$matrix: Counts matrix

Examples

if (FALSE) { # interactive()
annodb = load_annotations("hg38", canonical = T)

kmer_hist(annodb$seqs, "AAAAAAA")
}