kmeRtone: kmeRtone all-in-one user interface
In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

kmeRtone

R Documentation

kmeRtone all-in-one user interface

Description

This function serves as an all-in-one interface for various genomic data analyses leveraging k-mer based techniques.

Usage

kmeRtone(
  case.coor.path,
  genome.name,
  strand.sensitive,
  k,
  ctrl.rel.pos = c(80, 500),
  case.pattern,
  output.dir = "output/",
  case,
  genome,
  control,
  control.path,
  genome.path,
  rm.case.kmer.overlaps,
  single.case.len,
  merge.replicates,
  kmer.table,
  module = "score",
  rm.dup = TRUE,
  case.coor.1st.idx = 1,
  ctrl.coor.1st.idx = 1,
  coor.load.limit = 1,
  genome.load.limit = 1,
  genome.fasta.style = "UCSC",
  genome.ncbi.db = "refseq",
  use.UCSC.chr.name = FALSE,
  verbose = TRUE,
  kmer.cutoff = 5,
  selected.extremophiles,
  other.extremophiles,
  cosmic.username,
  cosmic.password,
  tumour.type.regex = NULL,
  tumour.type.exact = NULL,
  cell.type = "somatic",
  genic.elements.counts.dt,
  population.size = 1e+06,
  selected.genes,
  add.to.existing.population = FALSE,
  population.snv.dt = NULL,
  pop.plot = TRUE,
  pop.loop.chr = FALSE
)

Arguments

`case.coor.path`	Path to a folder containing chromosome-separated coordinate files or bedfiles. Assumed replicates for subfolder or bedfiles.
`genome.name`	Name of the genome (e.g., "hg19", "hg38"). Default is "unknown".
`strand.sensitive`	Logical value indicating whether strand polarity matters. Default is TRUE.
`k`	Length of k-mer to be investigated. Recommended values are 7 or 8.
`ctrl.rel.pos`	A vector of two integers specifying the relative range positions of control regions.
`case.pattern`	Regular expression pattern for identifying case regions. Default is NULL.
`output.dir`	Directory path for saving output files. Default is "output/".
`case`	Optional pre-built Coordinate object.
`genome`	Optional pre-built Genome object.
`control`	Optional pre-built control Coordinate object.
`control.path`	Path for pre-built control Coordinate object.
`genome.path`	Path to a directory of user-provided genome FASTA files.
`rm.case.kmer.overlaps`	Logical indicating whether to remove overlapping k-mers in case regions. Default is FALSE.
`single.case.len`	Integer indicating uniform length of case regions.
`merge.replicates`	Logical indicating whether to merge replicates. Default is TRUE.
`kmer.table`	Pre-calculated k-mer score table.
`module`	Selected kmeRtone module to run. Possible values include "score", "explore", "tune", among others.
`rm.dup`	Logical indicating whether to remove duplicate coordinates. Default is TRUE.
`case.coor.1st.idx`	Integer specifying indexing format for case coordinates.
`ctrl.coor.1st.idx`	Integer specifying indexing format for control coordinates.
`coor.load.limit`	Maximum number of coordinates to load. Default is 1.
`genome.load.limit`	Maximum number of genome sequences to load. Default is 1.
`genome.fasta.style`	String specifying the style of the genome FASTA. Possible values are "UCSC", "NCBI". Default is "UCSC".
`genome.ncbi.db`	String specifying the NCBI database to use. Possible values are "refseq", "genbank". Default is "refseq".
`use.UCSC.chr.name`	Logical indicating whether to use UCSC chromosome names.
`verbose`	Logical indicating whether to display progress messages. Default is TRUE.
`kmer.cutoff`	Cutoff percentage for k-mer selection in case studies. Default is 5.
`selected.extremophiles`	Vector of selected extremophile species for study.
`other.extremophiles`	Vector of other extremophile species for control.
`cosmic.username`	COSMIC username for accessing the cancer gene census.
`cosmic.password`	COSMIC password for accessing the cancer gene census.
`tumour.type.regex`	Regular expression pattern for filtering tumour types.
`tumour.type.exact`	Exact tumour type to be included in the cancer gene census.
`cell.type`	Cell type to be included in the cancer gene census. Default is "somatic".
`genic.elements.counts.dt`	Data table of susceptible k-mer counts in genic elements.
`population.size`	Size of the population for cross-population studies. Default is 1 million.
`selected.genes`	Selected genes for mutation in cross-population studies.
`add.to.existing.population`	Logical indicating whether to add to the existing simulated population. Default is FALSE.
`population.snv.dt`	Data table of single nucleotide variants used in population simulations.
`pop.plot`	Logical indicating whether to plot the outcome of the cross-population study. Default is TRUE.
`pop.loop.chr`	Logical indicating whether to loop based on chromosome name in cross-population studies. Default is FALSE.