Sparse Partial Correlations On Gene Expression

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Documentation for package ‘SPONGE’ version 1.0.3

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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