# Sparse Partial Correlations On Gene Expression

## Documentation for package ‘SPONGE’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ceRNA_interactions | ceRNA interactions
check_and_convert_expression_data | Checks if expression data is in matrix or ExpressionSet format and converts the latter to a standard matrix. Alternatively, a big.matrix descriptor object can be supplied to make use of shared memory between parallelized workers through the bigmemory package.
fn_elasticnet | Computes an elastic net model
fn_gene_miRNA_F_test | Perform F test for gene-miRNA elastic net model
fn_get_model_coef | Extract the model coefficients from an elastic net model
fn_get_rss | Compute the residual sum of squares error for an elastic net model
fn_get_shared_miRNAs | Identify miRNAs for which both genes have miRNA binding sites aka miRNA response elements in the competing endogeneous RNA hypothesis
genes_pairwise_combinations | Compute all pairwise interactions for a number of genes as indices
gene_expr | Gene expression test data set
mircode_ensg | mircode predicted miRNA gene interactions
mircode_symbol | mircode predicted miRNA gene interactions
mir_expr | miRNA expression test data set
mir_interactions | miRNA / gene interactions
precomputed_cov_matrices | covariance matrices under the null hypothesis that sensitivity correlation is zero
precomputed_null_model | A null model for testing purposes
sample_zero_mscor_cov | Sampling zero multiple miRNA sensitivity covariance matrices
sample_zero_mscor_data | Sample mscor coefficients from pre-computed covariance matrices
sponge | Compute competing endogeneous RNA interactions using Sparse Partial correlations ON Gene Expression (SPONGE)
sponge_build_null_model | Build null model for p-value computation
sponge_compute_p_values | Compute p-values for SPONGE interactions
sponge_edge_centralities | Computes edge centralities
sponge_gene_miRNA_interaction_filter | Determine miRNA-gene interactions to be considered in SPONGE
sponge_network | Prepare a sponge network for plotting
sponge_node_centralities | Computes various node centralities
sponge_plot_network | Plot a sponge network
sponge_plot_network_centralities | plot node network centralities
sponge_plot_simulation_results | Plot simulation results for different null models
sponge_run_benchmark | run sponge benchmark where various settings, i.e. with or without regression, single or pooled miRNAs, are compared.
sponge_subsampling | Sponge subsampling
targetscan_ensg | targetscan predicted miRNA gene interactions
targetscan_symbol | targetscan predicted miRNA gene interactions