Extending guilt by association by degree

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Documentation for package ‘EGAD’ version 1.37.0

• DESCRIPTION file.
• Package NEWS.

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