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

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

Usage

predict_msi_status(
  vcf_data_df,
  pcgr_data,
  msi_prediction_model,
  msi_prediction_dataset,
  target_size_mb,
  sample_name = "Test"
)

Arguments

vcf_data_df

data frame with somatic mutations/indels

pcgr_data

object with PCGR datasets

msi_prediction_model

statistical model for MSI prediction

msi_prediction_dataset

underlying dataset from TCGA used for development of statistical classifier

target_size_mb

size of targeted genomic region (coding)

sample_name

name of sample

Value

msi_data