sponge_compute_p_values {SPONGE} | R Documentation

## Compute p-values for SPONGE interactions

### Description

This method uses pre-computed covariance matrices that were created for various gene-gene correlations (0.2 to 0.9 in steps of 0.1) and number of miRNAs (between 1 and 8) under the null hypothesis that the sensitivity correlation is zero. Datasets are sampled from this null model and allow for an empirical p-value to be computed that is only significant if the sensitivity correlation is higher than can be expected by chance given the number of samples, correlation and number of miRNAs. p-values are adjusted indepdenently for each parameter combination using Benjamini-Hochberg FDR correction.

### Usage

    sponge_compute_p_values(sponge_result, null_model, log.level = "ERROR")

### Arguments

`sponge_result` | A data frame from a sponge call
`null_model` | optional, pre-computed simulated data
`log.level` | The log level of the logging package

### Value

A data frame with sponge results, now including p-values and adjusted p-value

### See Also

sponge_build_null_model

### Examples

    sponge_compute_p_values(ceRNA_interactions,
    null_model = precomputed_null_model)

[Package SPONGE version 1.12.0 Index]