Rerun CNV Calling with User-Defined Purity and Size Factor or Diploid Region

Allows users to rerun copy number variant (CNV) calling with custom purity and scale factor (size factor) values, or by specifying a diploid region for normalization.

Usage

RerunCNV(
  seg,
  input,
  models,
  call,
  gender,
  callcov = 0.3,
  dicovsf = NULL,
  purity = NULL,
  chromosome = NULL,
  start = NULL,
  end = NULL,
  mode = NULL,
  out_file
)

Arguments

seg

Character. Path to the AI segment file (e.g., *_GATK_AI_segment.tsv).

input

Character. Path to the top likelihood row file (e.g., *_top_likelihood_calls.tsv).

models

Character. Path to the model likelihood file (e.g., *_Models_likelihood.tsv).

call

Character. Path to the final call file.

gender

Character. Sample gender, either "male" or "female".

callcov

Numeric. Subclonal events calling cutoff based on coverage.

dicovsf

Numeric or character. Desired scale factor or range (e.g., 0.9, "0.9:1.1"). Optional.

purity

Numeric or character. Desired purity or range (e.g., 0.5, "0.5:0.7"). Optional.

chromosome

Character. Chromosome for diploid region (e.g., "1", "X"). Optional.

start

Integer. Start position for diploid region. Optional.

end

Integer. End position for diploid region. Optional.

mode

Character. Rerun mode: either "model" or "region".

out_file

Character. Output file path for the final calls.

Value

Invisibly returns the final call data frame.

Details

When mode = "region", chromosome must be set. If only chromosome and start are provided, the region spans from start to the end of the chromosome. If only chromosome and end are provided, the region spans from the start of the chromosome to end. If both start and end are given, the user-defined region is used.

When mode = "model", at least one of dicovsf or purity must be set. Both can be specified as single values or as ranges (e.g., "0.9:1.1").

This function enables re-calling of CNV segments using user-specified purity and/or size factor (SF), or by defining a diploid region for normalization. It supports both "model" and "region" rerun modes. The resulting calls are written to out_file.

Examples

if (FALSE) { # \dontrun{
# Rerun using a specific purity and size factor
RerunCNV(
  seg = "sample_GATK_AI_segment.tsv",
  input = "sample_top_likelihood_calls.tsv",
  models = "sample_Models_likelihood.tsv",
  call = "sample_final_call.tsv",
  gender = "female",
  dicovsf = "0.95:1.05",
  purity = "0.6:0.8",
  mode = "model",
  out_file = "sample_final_call_refined.tsv"
)

# Rerun using a user-defined diploid region
RerunCNV(
  seg = "sample_GATK_AI_segment.tsv",
  input = "sample_top_likelihood_calls.tsv",
  models = "sample_Models_likelihood.tsv",
  call = "sample_final_call.tsv",
  gender = "male",
  chromosome = "3",
  start = 1e6,
  end = 5e7,
  mode = "region",
  out_file = "sample_final_call_refined.tsv"
)
} # }