pred_refit_range {ICBioMark} | R Documentation |
Get Refitted Predictive Models for a First-Fit Range of Panels
Description
A function producing a refitted predictive model for each panel produced by usage of the function pred_first_fit(), by repeatedly applying the function pred_refit_panel().
Usage
pred_refit_range(
pred_first = NULL,
gene_lengths = NULL,
model = "T",
biomarker = "TMB",
marker_mut_types = c("NS", "I"),
training_data = NULL,
training_values = NULL,
mutation_vector = NULL,
t_s = NULL,
max_panel_length = NULL
)
Arguments
pred_first |
(list) A first-fit predictive model as produced by pred_first_fit(). |
gene_lengths |
(dataframe) A dataframe of gene lengths (see example_maf_data$gene_lengths for format). |
model |
(character) A choice of "T", "OLM" or "Count" specifying how predictions should be made. |
biomarker |
(character) If "TMB" or "TIB", automatically defines marker_mut_types, otherwise this will need to be specified separately. |
marker_mut_types |
(character) A vector specifying which mutation types groups determine the biomarker in question. |
training_data |
(sparse matrix) Training matrix, as produced by get_mutation_tables() (select train, val or test). |
training_values |
(dataframe) Training true values, as produced by get_biomarker_tables() (select train, val or test). |
mutation_vector |
(numeric) Optional vector specifying the values of the training matrix (training_data$matrix) in vector rather than matrix form. |
t_s |
(numeric) Optional vector specifying the frequencies of different mutation types. |
max_panel_length |
(numeric) Upper bound for panels to fit refitted models to. Most useful for "OLM" and "Count" model types. |
Value
A list with three elements:
fit, a list including a sparse matrix 'beta' giving prediction weights for each first-fit panel (one panel per column).
panel_genes, a sparse (logical) matrix giving the genes included in prediction for each first-fit panel.
panel_lengths, a vector giving the length of each first-fit panel.
Examples
example_refit_range <- pred_refit_range(pred_first = example_first_pred_tmb,
gene_lengths = example_maf_data$gene_lengths)