Man pages for EGAD
Extending guilt by association by degree

assortativityCalculating network assortativity
atrr.humanHuman GENCODE annotations (v22)
attr.mouseMouse GENCODE annotations (M7)
auc_multifuncCalculating AUC for functional groups from ranked lists
auprcArea under the precision recall curve
auroc_analyticArea under the receiver operating characteristic curve
biogridBIOGRID v3.4.126
build_binary_networkBuilds a binary network
build_coexp_expressionSetBuilds a coexpression network from an expressionSet
build_coexp_GEOIDBuilds a coexpression network given a GEO ID
build_coexp_networkBuilds a coexpression network from an expressionSet
build_semantic_similarity_networkBuilds a semantic similarity network
build_weighted_networkBuilds a weighted network
calculate_multifuncPerforming multifunctionality analysis
conv_smootherPlot smoothed curve
example_annotationsExample of annotations
example_binary_networkExample of binary network
example_coexpressionExample of binary network
example_neighbor_votingExample of binary network
extend_networkBuilds an extended network from a binary network
filter_networkFilter on matrix
filter_network_colsFilter on columns
filter_network_rowsFilter on rows
filter_orthologsFilter on orthologs
fmeasureFmeasure of precision-recall
genesGenes from BIOGRID v3.4.126
get_aucCalculates the area under a curve
get_biogridDownloading and filtering BIOGRID
get_countsGet counts
get_densityGet density
get_expression_data_gemmaObtain expression matrix from the GEMMA database
get_expression_matrix_from_GEOObtain expression matrix from GEO database
get_phenocartaDownloading and filtering Phenocarta
get_prcBuild precision-recall curve
get_rocBuild receiver operating characteristic curve
GO.humanGO - human
GO.mouseGO - mouse
GO.vocGene ontology vocabulary
make_annotationsCreating gene annotations
make_genelistCreating list of all genes in the data set.
make_gene_networkCreating gene-by-gene network
make_transparentMake a color transparent (Taken from an answer on...
neighbor_votingEvaluating Gene Function Prediction
node_degreeCalculate node degree
orthoGene orthologs
plot_densitiesPlot densities
plot_density_comparePlot density comparisons
plot_distributionPlot distribution histogram
plot_network_heatmapPlot network heatmap
plot_prcPlot precision recall curve
plot_rocPlot receiver operating characteristic curve
plot_roc_overlayPlot ROC overlay
plot_value_comparePlot value comparisons
predictionsPerforming Gene Function Prediction
repmatRep function for matrices
run_GBAPerforming 'Guilt by Association' Analysis
EGAD documentation built on Nov. 8, 2020, 8:31 p.m.