Sparse Partial Correlations On Gene Expression

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Documentation for package ‘SPONGE’ version 1.16.1

• 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