In c5sire/kmerize: K-Mer Tools for Building Databases

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
Sys.setenv("NOT_CRAN" = "true")

Count K-mers in FASTQ Files

We are using simulated k-mer data from the phi-X174 genome.

Getting the data and setting parameters:

suppressPackageStartupMessages(
  library(kmerize)
)


fq <- system.file("testdata/phix174-pe_w_err_5k_30q.fastq.gz", 
                  package = "kmerize")
k <- 9

out_file <- file.path(tempdir(), "phwei11")
out_db <- paste0(out_file, c(".kmc_pre", ".kmc_suf"))

Counting:

if (kmerize:::check_install_ok()) {
kmer_path = kmr_count(fq, out_file, 
                  k = k, 
                  f = "q" # file input format is fastq
                  )  
}

Convert to readable tabulated database:

if (kmerize:::check_install_ok()) {
kp <- kmr_write_tab(kmer_path)

kmers <- kmr_read_tab(kp)
head(kmers)
}

Genomic Response

# Getting the DNA
if (kmerize:::check_install_ok()) {
fp <- system.file("testdata/phix174.fasta", 
                  package = "kmerize")
dna <- Biostrings::readDNAStringSet(fp)

k <- as.integer(seq(3, 25, 2)) # currently k explicitly as integer sequence
res <- kmr_response(fp, k, fmt = "m")
res
}

if (kmerize:::check_install_ok()) {

kmr_plot_response(res, ref_k = 9, max_y = Biostrings::width(dna))
}

c5sire/kmerize documentation built on June 7, 2020, 9:26 p.m.