EGAD: Extending guilt by association by degree

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

Author
Sara Ballouz [aut, cre], Melanie Weber [aut, ctb], Paul Pavlidis [aut], Jesse Gillis [aut, ctb]
Date of publication
None
Maintainer
Sara Ballouz <sballouz@cshl.edu>
License
GPL-2
Version
1.2.0

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

Files in this package

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