SCORE: Calculate susceptibility scores for k-mers in case and control regions.

Description

Function calculates susceptibility scores for k-mers in case and control regions. Case regions are defined by genomic coordinates provided in a file or data.table. Control regions can be constructed relative to the case regions or provided directly. The scores are computed based on the occurrence of k-mers in case and control regions.

Usage

SCORE(
  case.coor.path,
  genome.name,
  strand.sensitive,
  k,
  ctrl.rel.pos,
  case.pattern,
  output.path,
  case,
  genome,
  control,
  control.path,
  genome.path,
  rm.case.kmer.overlaps,
  single.case.len,
  merge.replicates,
  rm.dup,
  case.coor.1st.idx,
  ctrl.coor.1st.idx,
  coor.load.limit,
  genome.load.limit,
  genome.fasta.style,
  genome.ncbi.db,
  use.UCSC.chr.name,
  verbose
)

Value

Data.table containing susceptibility scores for k-mers.

Arguments

case.coor.path: Path to the file containing genomic coordinates of case regions.
genome.name: Name of the genome to be used.
strand.sensitive: Logical indicating whether strand information should be considered.
k: Integer size of the expanded k-mer.
ctrl.rel.pos: Relative positions of control regions with respect to case regions. It should be a vector of two integers indicating the upstream and downstream distances from the case regions.
case.pattern: Regular expression pattern to identify the central sequence in case regions.
output.path: Directory path where the output files will be saved.
case: Data.table containing the genomic coordinates of case regions.
genome: Genome data.table containing the genomic sequence information.
control: Data.table containing the genomic coordinates of control regions.
control.path: Path to the file containing genomic coordinates of control regions (optional).
genome.path: Path to the genome FASTA file.
rm.case.kmer.overlaps: Logical indicating whether overlapping k-mers within case regions should be removed.
single.case.len: Single case length.
merge.replicates: Logical indicating whether replicates should be merged.
rm.dup: Logical indicating whether duplicate k-mers should be removed.
case.coor.1st.idx: First index in the case coordinate file.
ctrl.coor.1st.idx: First index in the control coordinate file.
coor.load.limit: Maximum number of coordinates to load.
genome.load.limit: Maximum number of genome sequences to load.
genome.fasta.style: FASTA style.
genome.ncbi.db: NCBI database.
use.UCSC.chr.name: Logical indicating whether to use UCSC chromosome names.
verbose: Logical indicating whether to display progress messages.