Count the k-mer frequency in a set of sequences

Count the k-mer frequency in a set of sequences

Usage

sequence_kmer_counts(
  seqs,
  tx2gene,
  out.path = NULL,
  path.basename = NULL,
  width = 7,
  step = 1,
  simplify.as = "matrix"
)

Arguments

seqs

Input Biostrings::DNAStringSet

tx2gene

Data frame mapping tx > gene with columsn tx_id + gene_id

out.path

Output directory path

path.basename

Output basename

width

K-mer size

step

step size

simplify.as

output type as either matrix or list

Value

oligonucleotide frequencies

Examples

if (FALSE) { # interactive()
}