kmr_compare

Compare k-mer sets

kmr_compare(in_files, cmp, ci = 2, cx = 1e+09, cs = 255)

Arguments

in_files	list of named file paths. The names are to be used in the comparison string.
cmp	a list containing a single named string with the kmer operations using the file short names.
ci	integer; min k cutoff value; default 2.
cx	integer; max k cutoff value; default 1e9.
cs	integer; max k count value; default 255.

Value

out_file

Details

The in_files list strings may contain parameter values for each in_file after the path.

Shorthand operator definitions: * intersect - subtract ~ counters_subtract + union

Highest priority: *. All other operators have equal priority.

Counter calculation modes are available for the oerators: *, ~, +. They are: min, max, diff, sum, left, right

References

Kokot M, Dlugosz M, Deorowicz S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics. 2017 Sep 1;33(17):2759-61.

See also

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

Examples

if (interactive()) {
  fa <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
    package = "kmerize"
  )
  fm <- system.file("testdata/phix174_m-pe_w_err_5k_30q.fastq.gz",
    package = "kmerize"
  )

  k <- 9
  tmd <- tempdir()
  if (!dir.exists(tmd)) dir.create(tmd)

  out_fx <- file.path(tmd, "phx")
  out_fm <- file.path(tmd, "phm")

  kmr_count(fa, out_fx, k = k, f = "q")
  kmr_count(fm, out_fm, k = k, f = "q")

  cmp_xy <- file.path(tmd, "cmp_xy")
}