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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.

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Version

Version

1.0.3

License

GPL-2

Maintainer

Sara Ballouz Developer

Last Published

February 15th, 2017

Functions in EGAD (1.0.3)

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