STUDY_ACROSS_SPECIES: Study k-mer composition across species.

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Study k-mer composition across species.

Description

Analysis of distribution of highly enriched k-mers across species.

Usage

STUDY_ACROSS_SPECIES(
  kmer.table,
  kmer.cutoff = 5,
  k,
  central.pattern = NULL,
  selected.extremophiles,
  other.extremophiles,
  output.dir = "study_across_species/",
  fasta.path
)

Arguments

kmer.table	A data.table of kmer table or path to it.
kmer.cutoff	Percentage of extreme kmers to study. Default to 5 percent.
k	K-mer size.
central.pattern	K-mer's central patterns. Default is NULL.
selected.extremophiles	A vector of selected extremophile species. e.g. c("Deinococcus soli", "Deinococcus deserti") The best representative will be selected from the assembly summary.
other.extremophiles	A vector of other extremophile species. These are used as a control to compare with the selected extremophiles.
output.dir	A directory for the outputs.
fasta.path	Path to a directory of user-provided genome FASTA files or the destination to save the NCBI/UCSC downloaded reference genome files.

Value

An output directory containing plots.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.