fit_gen_model: Fit Generative Model

In ICBioMark: Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers

Description

A function to fit a generative model to a mutation dataset. At its heart, requires a gene_lengths dataframe (for examples of the correct format for this see the pre-loaded datasets example_maf_data$gene_lengths and ensembl_gene_lengths), and a mutation dataset. This is best supplied through the 'table' argument, and constructed via the function get_mutation_tables().

Usage

fit_gen_model(
  gene_lengths,
  matrix = NULL,
  sample_list = NULL,
  gene_list = NULL,
  mut_types_list = NULL,
  col_names = NULL,
  table = NULL,
  nlambda = 100,
  n_folds = 10,
  maxit = 1e+09,
  seed_id = 1234,
  progress = FALSE,
  alt_model_type = NULL
)

Arguments

gene_lengths	(dataframe) A table with two columns: Hugo_Symbol and max_cds, providing the lengths of the genes to be modelled.
matrix	(Matrix::sparseMatrix) A mutation matrix, such as produced by the function get_table_from_maf().
sample_list	(character) The set of samples to be modelled.
gene_list	(character) The set of genes to be modelled.
mut_types_list	(character) The set of mutation types to be modelled.
col_names	(character) The column names of the 'matrix' parameter.
table	(list) Optional parameter combining matrix, sample_list, gene_list, mut_types_list, col_names, as is produced by the function get_tables().
nlambda	(numeric) The length of the vector of penalty weights, passed to the function glmnet::glmnet().
n_folds	(numeric) The number of cross-validation folds to employ.
maxit	(numeric) Technical parameter passed to the function glmnet::glmnet().
seed_id	(numeric) Input value for the function set.seed().
progress	(logical) Show progress bars and text.
alt_model_type	(character) Used to call an alternative generative model type such as "US" (no sample-dependent parameters) or "UI" (no gene/variant-type interactions).

Value

A list comprising three objects:

• An object 'fit', a fitted glmnet model.

• A table 'dev', giving average deviances for each regularisation penalty factor and cross-validation fold.

• An integer 's_min', the index of the regularsisation penalty minimising cross-validation deviance.

• A list 'names', containing the sample, gene, and mutation type information of the training data.

Examples

example_gen_model <- fit_gen_model(example_maf_data$gene_lengths, table = example_tables$train)
print(names(example_gen_model))

ICBioMark documentation built on Nov. 15, 2021, 5:09 p.m.