EXPLORE: Function generates various exploratory analyses.

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

Function generates various exploratory analyses.

Description

Function generates various exploratory analyses.

Usage

EXPLORE(
  case.coor.path,
  genome.name,
  strand.sensitive,
  k,
  case.pattern,
  output.path,
  case,
  genome,
  control,
  genome.path,
  single.case.len,
  rm.dup,
  case.coor.1st.idx,
  coor.load.limit,
  genome.load.limit,
  genome.fasta.style,
  genome.ncbi.db,
  use.UCSC.chr.name,
  verbose
)

Arguments

case.coor.path	Path to case coordinates.
genome.name	Genome name (e.g., hg19, hg38).
strand.sensitive	Boolean indicating if strand sensitivity is considered.
k	K-mer size.
case.pattern	String patterns to consider in the analysis.
output.path	Output directory path for exploration plots.
case	Coordinate class object or similar structure for case data.
genome	Genome class object or similar structure.
control	Control class object or similar structure.
genome.path	Path to genome fasta files.
single.case.len	Length of single cases.
rm.dup	Boolean indicating if duplicates should be removed.
case.coor.1st.idx	Indexing of case coordinates.
coor.load.limit	Maximum number of coordinates to load.
genome.load.limit	Maximum number of genome data to load.
genome.fasta.style	Fasta file style for genome data.
genome.ncbi.db	NCBI database for genome data.
use.UCSC.chr.name	Boolean indicating if UCSC chromosome naming is used.
verbose	Boolean indicating if verbose output is enabled.

Value

Output directory containing exploration plots.

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