Test samples using simple CASTLE model

Source: R/castle_simple.R

Tests samples for the presence of mutant DNA using the simple version of the CASTLE algorithm.

test_tumor_sample_simple(
  test_samples,
  simple_model,
  include_wildtype_CI = TRUE,
  include_mutant_CI = TRUE,
  alpha = 0.01
)

Arguments

test_samples

data.frame with samples to be tested as rows. At least the following columns should be present:

  • WildtypeOnlyDroplets

  • MutantOnlyDroplets

  • DoubleNegativeDroplets

  • DoublePositiveDroplets

If data from QuataSoft is available, these can be imported using import_QS_files.

simple_model

A fitted model as generated by train_simple_ddpcr_model.

include_wildtype_CI

Logical. Should confidence intervals for wild type DNA statistics be included? Default is TRUE.

include_mutant_CI

Logical. Should confidence intervals for mutant DNA statistics be included? Default is TRUE.

alpha

The alpha used for the statistical test and confidence intervals. Default is 0.01.

Value

A data.frame with results from the CASTLE algorithm (parameter estimates, CIs, p-values etc.) joined to the right of test_samples. Following is the full list of information added:

test_statistic/p_val

Log-likelihood-ratio test statistic/p-value from the statistical test for the presence of mutant DNA (H0: No mutant DNA, HA: Mutant DNA present).

mutation_detected

Logical. TRUE if the mutation is detected i.e. if the p-value < alpha.

allele_frequency

Estimated allele frequency of the mutant allele (error corrected).

allele_frequency_CI_[lower|upper]

Confidence interval for allele_frequency.

mutant_molecules_per_droplet

Estimated number of mutant molecules per droplet (error corrected).

mutant_molecules_per_droplet_CI_[lower|upper]

Confidence interval for mutant_molecules_per_droplet.

wildtype_molecules_per_droplet

Estimated number of wildtype molecules per droplet.

wildtype_molecules_per_droplet_CI_[lower|upper]

Confidence interval for wildtype_molecules_per_droplet.

total_mutant_molecules

Estimated total number of mutant molecules in sample (error corrected).

total_mutant_molecules_CI_[lower|upper]

Confidence interval for total_mutant_molecules.

total_wildtype_molecules

Estimated number of wildtype molecules per droplet.