sponge_run_benchmark: run sponge benchmark where various settings, i.e. with or...

In biomedbigdata/SPONGE: Sparse Partial Correlations On Gene Expression

run sponge benchmark where various settings, i.e. with or without regression, single or pooled miRNAs, are compared.

Description

run sponge benchmark where various settings, i.e. with or without regression, single or pooled miRNAs, are compared.

Usage

sponge_run_benchmark(
  gene_expr,
  mir_expr,
  mir_predicted_targets,
  number_of_samples = 100,
  number_of_datasets = 100,
  number_of_genes_to_test = c(25),
  compute_significance = FALSE,
  folder = NULL
)

Arguments

gene_expr	A gene expression matrix with samples in rows and featurs in columns. Alternatively an object of class ExpressionSet.
mir_expr	A miRNA expression matrix with samples in rows and features in columns. Alternatively an object of class ExpressionSet.
mir_predicted_targets	(a list of) mir interaction sources such as targetscan, etc.
number_of_samples	number of samples in the null model
number_of_datasets	number of datasets to sample from the null model
number_of_genes_to_test	a vector of numbers of genes to be tested, e.g. c(250,500)
compute_significance	whether to compute p-values
folder	where the results should be saved, if NULL no output to disk

Value

a list (regression, no regression) of lists (single miRNA, pooled miRNAs) of benchmark results

Examples

sponge_run_benchmark(gene_expr = gene_expr, mir_expr = mir_expr,
mir_predicted_targets = targetscan_symbol,
number_of_genes_to_test = c(10), folder = NULL)

biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.