kmr_response

k should be an odd number. In case of fastq files the file can also be in compressed format (e.g. *.fastq.tar.gz). This parameter will be inferred from the file name, if not set.

kmr_response(fastx, k = c(5, 7, 9, 11), fmt = NULL, ci = 0)

Arguments

fastx	a fastq or fasta formatted file
k	kmer size. One value or a sequence of values
fmt	type of input file, fasta = f, fasta with multiple lines = m, fastq = q
ci	cutoff value for min k

Value

data.frame with results

See also

Other kmer_help: kmr_compare(), kmr_length_fasta(), kmr_map_kmers(), kmr_plot_map(), kmr_plot_response(), kmr_position_coverage(), kmr_scan_k_min()

Examples

if (interactive()) {
  fa <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
    package = "kmerize"
  )
  k <- as.integer(seq(1, 3, 2))


  res <- kmr_response(fa, k, fmt = "q")
}