Man pages for SPONGE
Sparse Partial Correlations On Gene Expression

ceRNA_interactionsceRNA interactions
check_and_convert_expression_dataChecks if expression data is in matrix or ExpressionSet...
fn_elasticnetComputes an elastic net model
fn_gene_miRNA_F_testPerform F test for gene-miRNA elastic net model
fn_get_model_coefExtract the model coefficients from an elastic net model
fn_get_rssCompute the residual sum of squares error for an elastic net...
fn_get_shared_miRNAsIdentify miRNAs for which both genes have miRNA binding sites...
gene_exprGene expression test data set
genes_pairwise_combinationsCompute all pairwise interactions for a number of genes as...
mircode_ensgmircode predicted miRNA gene interactions
mircode_symbolmircode predicted miRNA gene interactions
mir_exprmiRNA expression test data set
mir_interactionsmiRNA / gene interactions
precomputed_cov_matricescovariance matrices under the null hypothesis that...
precomputed_null_modelA null model for testing purposes
sample_zero_mscor_covSampling zero multiple miRNA sensitivity covariance matrices
sample_zero_mscor_dataSample mscor coefficients from pre-computed covariance...
spongeCompute competing endogeneous RNA interactions using Sparse...
sponge_build_null_modelBuild null model for p-value computation
sponge_compute_p_valuesCompute p-values for SPONGE interactions
sponge_edge_centralitiesComputes edge centralities
sponge_gene_miRNA_interaction_filterDetermine miRNA-gene interactions to be considered in SPONGE
sponge_networkPrepare a sponge network for plotting
sponge_node_centralitiesComputes various node centralities
sponge_plot_networkPlot a sponge network
sponge_plot_network_centralitiesplot node network centralities
sponge_plot_simulation_resultsPlot simulation results for different null models
sponge_run_benchmarkrun sponge benchmark where various settings, i.e. with or...
sponge_subsamplingSponge subsampling
targetscan_ensgtargetscan predicted miRNA gene interactions
targetscan_symboltargetscan predicted miRNA gene interactions
SPONGE documentation built on Nov. 8, 2020, 5:39 p.m.