# Extending guilt by association by degree

## Documentation for package ‘EGAD’ version 1.40.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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