PPInfer-package {PPInfer}R Documentation

Inferring functionally related proteins using protein interaction networks

Description

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

Details

The DESCRIPTION file:

Package: PPInfer
Type: Package
Title: Inferring functionally related proteins using protein interaction networks
Description: Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.
Version: 1.20.3
Date: 2021-11-23
Author: Dongmin Jung, Xijin Ge
Maintainer: Dongmin Jung <dmdmjung@gmail.com>
Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData
Imports: httr
Suggests:
License: Artistic-2.0
biocViews: Software, StatisticalMethod, Network, GraphAndNetwork, GeneSetEnrichment, NetworkEnrichment, Pathways
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/PPInfer
git_branch: RELEASE_3_14
git_last_commit: 5c224c6
git_last_commit_date: 2021-11-23
Date/Publication: 2021-11-25

Index of help topics:

GSEA.barplot            Visualize the gene set enrichment analysis
ORA                     Over-representation Analysis
ORA.barplot             Visualize the over-representation analysis
PPInfer-package         Inferring functionally related proteins using
                        protein interaction networks
enrich.net              Visualize network for the functional enrichment
                        analysis
net.infer               Inferring functionally related proteins using
                        networks
net.infer.ST            Inferring functionally related proteins with
                        self training
net.kernel              Kernel matrix for a graph
ppi.infer.human         Inferring functionally related proteins using
                        protein networks for human
ppi.infer.mouse         Inferring functionally related proteins using
                        protein networks for mouse
self.train.kernel       Self training for a kernel matrix

Further information is available in the following vignettes:

PPInfer User manual (source, pdf)

Author(s)

Dongmin Jung, Xijin Ge

Maintainer: Dongmin Jung <dmdmjung@gmail.com>


[Package PPInfer version 1.20.3 Index]