Function that predicts MSI status based on fraction of indels among calls

Usage

predict_msi_status(
  variant_set,
  ref_data,
  msi_prediction_model,
  msi_prediction_dataset,
  msi_feature_variance_table = NULL,
  target_size_mb,
  n_calls = NA_integer_,
  sample_name = "Test"
)

Arguments

variant_set: data frame with somatic mutations/indels
ref_data: PCGR reference data object
msi_prediction_model: statistical model for MSI prediction
msi_prediction_dataset: underlying dataset from TCGA used for development of statistical classifier
msi_feature_variance_table: lookup table (from model training) mapping mutation-count bins to expected feature SD; used to qualify prediction confidence. NULL if not available.
target_size_mb: size of targeted genomic region (coding)
n_calls: number of variants passed to the classifier
sample_name: name of sample

Value

msi_data