kmr_map_kmers

kmr_map_kmers

kmr_map_kmers(kmers, genome, seqname = NULL)

Arguments

kmers	kmer table
genome	a path to a fasta sequence
seqname	name of the sequence

Value

GRange object of mapped kmers

See also

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

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

Examples

if (interactive()) {

  fa <- system.file("testdata/phix174.fasta", package = "kmerize")
  a <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz",
                   package = "kmerize")
  b <- system.file("testdata/phix174_m-pe_w_err_5k_30q.fastq.gz",
                   package = "kmerize")

  x <- kmr_scan_k_min(a, b, k = 9, min_kmers = 3, cleanup = FALSE)
  rr <- kmr_read_rds(x$kmer_tbl)


  kmap <- kmr_map_kmers(rr, genome = fa, "phi-X174")
  kmap
}