kmr_position_coverage

Scans a set of mapped kmers if they fall around a position. Returns a summary table for each k which includes the coverage and the start and beginning of the range.

kmr_position_coverage(
  kmers = NULL,
  pos = NULL,
  fasta = fasta,
  min_coverage = 5
)

Arguments

kmers	a list object as returned from kmr_scan_k_min
pos	a position from the reference genome
fasta	a path to a fasta sequence file (for example a reference chromosome)
min_coverage	a desirable level of minimum coverage

Value

data.frame

See also

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

Examples

if (interactive()) {

  # Reference genome
  fasta <- system.file("testdata/phix174.fasta", package = "kmerize")

  # Simulated NGS files from reference sequence and a modified sequence.
  # The modification is a SNP at position 911.

  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"
  )


  kmers <- kmr_scan_k_min(a, b,
    k = seq(5, 15, 2),
    min_kmers = 1,
    cleanup = FALSE,
    ci = 0,
    cx = 1000
  )

  kmr_position_coverage(kmers, pos = 911, fasta = fasta, min_coverage = 5)
}