sponge_run_benchmark {SPONGE} | R Documentation

## 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)

[Package SPONGE version 1.12.0 Index]