EGAD: Extending guilt by association by degree

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

AuthorSara Ballouz [aut, cre], Melanie Weber [aut, ctb], Paul Pavlidis [aut], Jesse Gillis [aut, ctb]
Date of publicationNone
MaintainerSara Ballouz <sballouz@cshl.edu>
LicenseGPL-2
Version1.2.0

View on Bioconductor

Man pages

assortativity: Calculating network assortativity

atrr.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...

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

Functions

assortativity Man page
attr.human Man page
attr.mouse Man page
auc_multifunc Man page
auprc Man page
auroc_analytic Man page
biogrid Man page
build_binary_network Man page
build_coexp_expressionSet Man page
build_coexp_GEOID Man page
build_coexp_network Man page
build_semantic_similarity_network Man page
build_weighted_network Man page
calculate_multifunc Man page
conv_smoother Man page
example_annotations Man page
example_binary_network Man page
example_coexpression Man page
example_neighbor_voting Man page
extend_network Man page
filter_network Man page
filter_network_cols Man page
filter_network_rows Man page
filter_orthologs Man page
fmeasure Man page
genes Man page
get_auc Man page
get_biogrid Man page
get_counts Man page
get_density Man page
get_expression_data_gemma Man page
get_expression_matrix_from_GEO Man page
get_phenocarta Man page
get_prc Man page
get_roc Man page
GO.human Man page
GO.mouse Man page
GO.voc Man page
make_annotations Man page
make_genelist Man page
make_gene_network Man page
make_transparent Man page
neighbor_voting Man page
node_degree Man page
ortho Man page
pheno Man page
plot_densities Man page
plot_density_compare Man page
plot_distribution Man page
plot_network_heatmap Man page
plot_prc Man page
plot_roc Man page
plot_roc_overlay Man page
plot_value_compare Man page
predictions Man page
repmat Man page
run_GBA Man page

Files

EGAD/DESCRIPTION
EGAD/NAMESPACE
EGAD/R
EGAD/R/GO.human.R EGAD/R/GO.mouse.R EGAD/R/GO.voc.R EGAD/R/assortativity.R EGAD/R/attr.human.R EGAD/R/attr.mouse.R EGAD/R/auc_multifunc.R EGAD/R/auprc.R EGAD/R/auroc_analytic.R EGAD/R/biogrid.R EGAD/R/build_binary_network.R EGAD/R/build_coexp_GEOID.R EGAD/R/build_coexp_expressionSet.R EGAD/R/build_coexp_network.R EGAD/R/build_semantic_similarity_network.R EGAD/R/build_weighted_network.R EGAD/R/calculate_multifunc.R EGAD/R/conv_smoother.R EGAD/R/example_annotations.R EGAD/R/example_binary_network.R EGAD/R/example_coexpression.R EGAD/R/example_neighbor_voting.R EGAD/R/extend_network.R EGAD/R/filter_network.R EGAD/R/filter_network_cols.R EGAD/R/filter_network_rows.R EGAD/R/filter_orthologs.R EGAD/R/fmeasure.R EGAD/R/genes.R EGAD/R/get_auc.R EGAD/R/get_biogrid.R EGAD/R/get_counts.R EGAD/R/get_density.R EGAD/R/get_expression_data_gemma.R EGAD/R/get_expression_matrix_from_GEO.R EGAD/R/get_phenocarta.R EGAD/R/get_prc.R EGAD/R/get_roc.R EGAD/R/make_annotations.R EGAD/R/make_gene_network.R EGAD/R/make_genelist.R EGAD/R/make_transparent.R EGAD/R/neighbor_voting.R EGAD/R/node_degree.R EGAD/R/ortho.R EGAD/R/pheno.R EGAD/R/plot_densities.R EGAD/R/plot_density_compare.R EGAD/R/plot_distribution.R EGAD/R/plot_network_heatmap.R EGAD/R/plot_prc.R EGAD/R/plot_roc.R EGAD/R/plot_roc_overlay.R EGAD/R/plot_value_compare.R EGAD/R/predictions.R EGAD/R/repmat.R EGAD/R/run_GBA.R
EGAD/build
EGAD/build/vignette.rds
EGAD/data
EGAD/data/GO.human.RData
EGAD/data/GO.mouse.RData
EGAD/data/GO.voc.RData
EGAD/data/attr.human.RData
EGAD/data/attr.mouse.RData
EGAD/data/biogrid.RData
EGAD/data/datalist
EGAD/data/example_annotations.RData
EGAD/data/example_binary_network.RData
EGAD/data/example_coexpression.RData
EGAD/data/example_neighbor_voting.RData
EGAD/data/genes.RData
EGAD/data/ortho.RData
EGAD/data/pheno.RData
EGAD/inst
EGAD/inst/NEWS
EGAD/inst/doc
EGAD/inst/doc/EGAD.R
EGAD/inst/doc/EGAD.Rmd
EGAD/inst/doc/EGAD.pdf
EGAD/man
EGAD/man/GO.human.Rd EGAD/man/GO.mouse.Rd EGAD/man/GO.voc.Rd EGAD/man/assortativity.Rd EGAD/man/atrr.human.Rd EGAD/man/attr.mouse.Rd EGAD/man/auc_multifunc.Rd EGAD/man/auprc.Rd EGAD/man/auroc_analytic.Rd EGAD/man/biogrid.Rd EGAD/man/build_binary_network.Rd EGAD/man/build_coexp_GEOID.Rd EGAD/man/build_coexp_expressionSet.Rd EGAD/man/build_coexp_network.Rd EGAD/man/build_semantic_similarity_network.Rd EGAD/man/build_weighted_network.Rd EGAD/man/calculate_multifunc.Rd EGAD/man/conv_smoother.Rd EGAD/man/example_annotations.Rd EGAD/man/example_binary_network.Rd EGAD/man/example_coexpression.Rd EGAD/man/example_neighbor_voting.Rd EGAD/man/extend_network.Rd EGAD/man/filter_network.Rd EGAD/man/filter_network_cols.Rd EGAD/man/filter_network_rows.Rd EGAD/man/filter_orthologs.Rd EGAD/man/fmeasure.Rd EGAD/man/genes.Rd EGAD/man/get_auc.Rd EGAD/man/get_biogrid.Rd EGAD/man/get_counts.Rd EGAD/man/get_density.Rd EGAD/man/get_expression_data_gemma.Rd EGAD/man/get_expression_matrix_from_GEO.Rd EGAD/man/get_phenocarta.Rd EGAD/man/get_prc.Rd EGAD/man/get_roc.Rd EGAD/man/make_annotations.Rd EGAD/man/make_gene_network.Rd EGAD/man/make_genelist.Rd EGAD/man/make_transparent.Rd EGAD/man/neighbor_voting.Rd EGAD/man/node_degree.Rd EGAD/man/ortho.Rd EGAD/man/pheno.Rd EGAD/man/plot_densities.Rd EGAD/man/plot_density_compare.Rd EGAD/man/plot_distribution.Rd EGAD/man/plot_network_heatmap.Rd EGAD/man/plot_prc.Rd EGAD/man/plot_roc.Rd EGAD/man/plot_roc_overlay.Rd EGAD/man/plot_value_compare.Rd EGAD/man/predictions.Rd EGAD/man/repmat.Rd EGAD/man/run_GBA.Rd
EGAD/tests
EGAD/tests/testthat
EGAD/tests/testthat.R
EGAD/tests/testthat/test.auroc.r
EGAD/tests/testthat/test.mf.r
EGAD/tests/testthat/test.network.r
EGAD/tests/testthat/test.nv.r
EGAD/vignettes
EGAD/vignettes/EGAD.Rmd
EGAD/vignettes/EGAD.bib
EGAD/vignettes/figures
EGAD/vignettes/figures/figure_GO_comb.png
EGAD/vignettes/figures/figure_aurocs_comparisons.png
EGAD/vignettes/figures/figure_benchmark.png
EGAD/vignettes/figures/figure_degree_corr.png
EGAD/vignettes/figures/figure_indirect.png
EGAD/vignettes/figures/figure_mf.png
EGAD/vignettes/figures/figure_mf_yeast_human.png
EGAD/vignettes/figures/figure_nd_yeast_human.png
EGAD/vignettes/figures/figure_nv.png
EGAD/vignettes/figures/figure_nv_yeast_human.png
EGAD/vignettes/figures/figure_overlay.png
EGAD/vignettes/figures/figure_pheno_comb.png
EGAD/vignettes/figures/figure_pheno_degree_corr.png
EGAD/vignettes/figures/figure_pheno_mf.png
EGAD/vignettes/figures/figure_pheno_nv.png
EGAD/vignettes/figures/figure_smoother.png
EGAD/vignettes/figures/gba_schematic_resized.png
EGAD/vignettes/figures/labels_resized.png
EGAD/vignettes/figures/mf_schematic.png
EGAD/vignettes/figures/network_resized.png
EGAD/vignettes/figures/overview_resized.png

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