RDocumentation
Moon
Learn R
Search all packages and functions
EGAD (version 1.0.3)
Extending guilt by association by degree
Description
The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.
Copy Link
Copy
Link to current version
Version
Version
1.0.3
1.0.2
Down Chevron
Version
1.0.3
License
GPL-2
Maintainer
Sara Ballouz Developer
Last Published
April 20th, 2016
Functions in EGAD (1.0.3)
Search functions
build_coexp_expressionSet
Builds a coexpression network from an expressionSet
example_binary_network
Example of binary network
build_coexp_GEOID
Builds a coexpression network given a GEO ID
GO.mouse
GO - mouse
example_coexpression
Example of binary network
GO.voc
Gene ontology vocabulary
plot_distribution
Plot distribution histogram
plot_network_heatmap
Plot network heatmap
biogrid
BIOGRID v3.4.126
build_binary_network
Builds a binary network
build_coexp_network
Builds a coexpression network from an expressionSet
fmeasure
Fmeasure of precision-recall
build_semantic_similarity_network
Builds a semantic similarity network
genes
Genes from BIOGRID v3.4.126
get_expression_matrix_from_GEO
Obtain expression matrix from GEO database
get_expression_data_gemma
Obtain expression matrix from the GEMMA database
ortho
Gene orthologs
pheno
Phenocarta
plot_prc
Plot precision recall curve
plot_roc_overlay
Plot ROC overlay
assortativity
Calculating network assortativity
attr.human
Human GENCODE annotations (v22)
conv_smoother
Plot smoothed curve
example_annotations
Example of annotations
filter_network_cols
Filter on columns
filter_network_rows
Filter on rows
get_phenocarta
Downloading and filtering Phenocarta
get_prc
Build precision-recall curve
predictions
Performing Gene Function Prediction
repmat
Rep function for matrices
get_counts
Get counts
get_roc
Build receiver operating characteristic curve
get_density
Get density
GO.human
GO - human
make_genelist
Creating list of all genes in the data set.
make_transparent
Make a color transparent (Taken from an answer on StackOverflow by Nick Sabbe)
attr.mouse
Mouse GENCODE annotations (M7)
auc_multifunc
Calculating AUC for functional groups from ranked lists
build_weighted_network
Builds a weighted network
calculate_multifunc
Performing multifunctionality analysis
get_auc
Calculates the area under a curve
get_biogrid
Downloading and filtering BIOGRID
neighbor_voting
Evaluating Gene Function Prediction
node_degree
Calculate node degree
plot_roc
Plot receiver operating characteristic curve
plot_value_compare
Plot value comparisons
auprc
Area under the precision recall curve
auroc_analytic
Area under the receiver operating characteristic curve
example_neighbor_voting
Example of binary network
extend_network
Builds an extended network from a binary network
filter_network
Filter on matrix
filter_orthologs
Filter on orthologs
plot_densities
Plot densities
make_annotations
Creating gene annotations
make_gene_network
Creating gene-by-gene network
plot_density_compare
Plot density comparisons
run_GBA
Performing 'Guilt by Association' Analysis