Package: fgga 1.15.0

Flavio Spetale

fgga: Hierarchical ensemble method based on factor graph

Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.

Authors:Flavio Spetale [aut, cre]

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fgga.pdf |fgga.html✨
fgga/json (API)
NEWS

# Install 'fgga' in R:

install.packages('fgga', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fspetale/fgga/issues

Datasets:

CfData - A set of characterized protein coding genes from the Cannis familiaris organism annotated to a target GO subgraph considering both experimental and electronic evidence.

On BioConductor:fgga-1.15.0(bioc 3.21)fgga-1.14.0(bioc 3.20)

software statisticalmethod classification network networkinference supportvectormachine graphandnetwork go

4.65 score 3 stars 6 scripts 141 downloads 13 exports 55 dependencies

Last updated 21 days agofrom:df196425be. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	OK	Nov 19 2024
R-4.5-linux	OK	Nov 19 2024
R-4.4-win	OK	Nov 19 2024
R-4.4-mac	OK	Nov 19 2024
R-4.3-win	OK	Nov 19 2024
R-4.3-mac	OK	Nov 19 2024

Exports:createFolds fgga fgga2bipartite fHierarchicalMeasures fMeasures fMeasuresByLevel maxDistancegraphOnto msgFGGA preCoreFG svmOnto svmTrain tableTPG varianceOnto

Dependencies:askpass BH BiocFileCache BiocGenerics bit bit64 blob cachem class cli cpp11 curl DBI dbplyr dplyr e1071 fansi fastmap filelock generics glue graph gRbase httr igraph jsonlite lattice lifecycle magrittr MASS Matrix memoise mime openssl pillar pkgconfig plogr proxy purrr R6 RBGL Rcpp RcppArmadillo RcppEigen rlang RSQLite stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr

FGGA: Factor Graph GO Annotation

F.E. Spetale, E. Tapia

Rendered fromfgga.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-08-17
Started: 2021-04-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
FGGA: Factor Graph Gene ontology Annotation.	fgga-package
A set of characterized protein coding genes from the Cannis familiaris organism annotated to a target GO subgraph considering both experimental and electronic evidence.	CfData
Data splitting function useful for binary classification tasks	createFolds
Factor Graph Cross-Ontology Annotation model	fgga
Forney Factor Graph model	fgga2bipartite
Individual and hierarchical F-measures	fHierarchicalMeasures fMeasures fMeasuresByLevel
Maximum distance for a graph	maxDistancegraphOnto
Transitive closure processing of a cross-ontology DAG	preCoreFG
Message passing algorithm between nodes of the Forney Factor Graph	msgFGGA
Ontology-term predictions by binary SVM classifiers	svmOnto
Binary SVM classification models for individual Ontology-term predictions	svmTrain
Valid configurations for hidden variable nodes in a Forney Factor Graph	tableTPG
The variance of the gaussian learning noise at individual Ontology-terms	varianceOnto