EXPLORE: 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
)

Value

Output directory containing exploration plots.

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.