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Assign Copy Number Call Without Model

Source: R/cnvutils.R
CallwoModel.Rd

Assigns a copy number call ("GAIN", "LOSS", "REF", "GAINLOH", or "CNLOH") to a segment based on corrected copy number fraction (CNF), minor allele frequency (MAF), and probe characteristics, using user-defined thresholds.

Usage

CallwoModel(
  chromosome,
  CNF_correct,
  MAF_correct,
  MAF_gmm_G,
  MAF_Probes,
  MAF_gmm_weight,
  callcovcutoff = 0.3,
  callaicutoff = 0.3,
  minsnpcallaicutoff = 10,
  gender
)

Arguments

chromosome

Character. Chromosome name (e.g., "1", "X", "Y").

CNF_correct

Numeric. Corrected copy number fraction (CNF).

MAF_correct

Numeric. Corrected minor allele frequency (MAF).

MAF_gmm_G

Integer. Number of GMM clusters (not directly used in logic, but included for compatibility).

MAF_Probes

Integer. Number of probes used for MAF estimation.

MAF_gmm_weight

Numeric. GMM weight (not directly used in logic, but included for compatibility).

callcovcutoff

Numeric. Threshold for CNF to call gain or loss (default: 0.3).

callaicutoff

Numeric. Threshold for MAF to call gain with loss of heterozygosity (GAINLOH) (default: 0.3).

minsnpcallaicutoff

Integer. Minimum number of SNP probes to call CNLOH (default: 10).

gender

Character. Gender information "male" or "female".

Value

Character. Copy number call: one of "GAIN", "LOSS", "REF", "GAINLOH", or "CNLOH".

Details

Calls are made according to CNF and MAF thresholds:

  • For sex chromosomes in males, thresholds are adjusted for haploid status.

  • "GAINLOH" is called if CNF is high and MAF is below a dynamic cutoff.

  • "CNLOH" is called if MAF is low and probe count meets the minimum threshold.

Examples

CallwoModel("1", CNF_correct = 2.8, MAF_correct = 0.1, MAF_gmm_G = 2, MAF_Probes = 15, MAF_gmm_weight = 0.5, gender = "female")
#> [1] "GAINLOH"