Extending guilt by association by degree

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Documentation for package ‘EGAD’ version 1.18.0

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assortativity Calculating network assortativity
attr.human Human GENCODE annotations (v22)
attr.mouse Mouse GENCODE annotations (M7)
auc_multifunc Calculating AUC for functional groups from ranked lists
auprc Area under the precision recall curve
auroc_analytic Area under the receiver operating characteristic curve
biogrid BIOGRID v3.4.126
build_binary_network Builds a binary network
build_coexp_expressionSet Builds a coexpression network from an expressionSet
build_coexp_GEOID Builds a coexpression network given a GEO ID
build_coexp_network Builds a coexpression network from an expressionSet
build_semantic_similarity_network Builds a semantic similarity network
build_weighted_network Builds a weighted network
calculate_multifunc Performing multifunctionality analysis
conv_smoother Plot smoothed curve
example_annotations Example of annotations
example_binary_network Example of binary network
example_coexpression Example of binary network
example_neighbor_voting Example of binary network
extend_network Builds an extended network from a binary network
filter_network Filter on matrix
filter_network_cols Filter on columns
filter_network_rows Filter on rows
filter_orthologs Filter on orthologs
fmeasure Fmeasure of precision-recall
genes Genes from BIOGRID v3.4.126
get_auc Calculates the area under a curve
get_biogrid Downloading and filtering BIOGRID
get_counts Get counts
get_density Get density
get_expression_data_gemma Obtain expression matrix from the GEMMA database
get_expression_matrix_from_GEO Obtain expression matrix from GEO database
get_phenocarta Downloading and filtering Phenocarta
get_prc Build precision-recall curve
get_roc Build receiver operating characteristic curve
GO.human GO - human
GO.mouse GO - mouse
GO.voc Gene ontology vocabulary
make_annotations Creating gene annotations
make_genelist Creating list of all genes in the data set.
make_gene_network Creating gene-by-gene network
make_transparent Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
neighbor_voting Evaluating Gene Function Prediction
node_degree Calculate node degree
ortho Gene orthologs
pheno Phenocarta
plot_densities Plot densities
plot_density_compare Plot density comparisons
plot_distribution Plot distribution histogram
plot_network_heatmap Plot network heatmap
plot_prc Plot precision recall curve
plot_roc Plot receiver operating characteristic curve
plot_roc_overlay Plot ROC overlay
plot_value_compare Plot value comparisons
predictions Performing Gene Function Prediction
repmat Rep function for matrices
run_GBA Performing 'Guilt by Association' Analysis