sponge_run_benchmark: run sponge benchmark where various settings, i.e. with or...
In SPONGE: Sparse Partial Correlations On Gene Expression

Description Usage Arguments Value Examples

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

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)

`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

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

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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)