build_classifier_central_genes: build classifiers for central genes

View source: R/fn_spongeffects_utility.R

build_classifier_central_genesR Documentation

build classifiers for central genes

Description

build classifiers for central genes

Usage

build_classifier_central_genes(
  train_gene_expr,
  test_gene_expr,
  train_enrichment_modules,
  test_enrichment_modules,
  train_meta_data,
  test_meta_data,
  train_meta_data_type = "TCGA",
  test_meta_data_type = "TCGA",
  metric = "Exact_match",
  tunegrid_c = c(1:100),
  n.folds = 10,
  repetitions = 3
)

Arguments

train_gene_expr

expression data of train dataset, genenames must be in rownames

test_gene_expr

expression data of test dataset, genenames must be in rownames

train_enrichment_modules

return of enrichment_modules()

test_enrichment_modules

return of enrichment_modules()

train_meta_data

meta data of train dataset

test_meta_data

meta data of test dataset

train_meta_data_type

TCGA or METABRIC

test_meta_data_type

TCGA or METABRIC

metric

metric (Exact_match, Accuracy) (default: Exact_match)

tunegrid_c

defines the grid for the hyperparameter optimization during cross validation (caret package) (default: 1:100)

n.folds

number of folds to be calculated

repetitions

number of k-fold cv iterations (default: 3)

Value

model for central genes


mlist/SPONGE documentation built on Feb. 12, 2023, 1:22 a.m.