mdgsa: Multi Dimensional Gene Set Analysis.
Version 1.8.0

Functions to preform a Gene Set Analysis in several genomic dimensions. Including methods for miRNAs.

Browse man pages Browse package API and functions Browse package files

AuthorDavid Montaner <dmontaner@cipf.es>
Bioconductor views Annotation GO GeneSetEnrichment Pathways
Date of publicationNone
MaintainerDavid Montaner <dmontaner@cipf.es>
LicenseGPL
Version1.8.0
URL https://github.com/dmontaner/mdgsa http://www.dmontaner.com
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mdgsa")

Man pages

annotFilter: Checks and filters an annotation list.
annotList2mat: Convert an annotation list into an annotation matrix.
annotMat2list: Convert an annotation matrix into an annotation list.
getGOnames: Get Gene Ontology names
getKEGGnames: Get KEGG names
getOntology: Get GO term Ontology
goLeaves: Keep just leaf nodes from the Gene Ontology DAG.
indexTransform: Transform ranking index distribution.
mdGsa: Multi-Dimensional Gene Set Analysis.
mdPat: Multi-Dimensional Gene Set Analysis Pattern Classification.
plotMdGsa: Plot Multi-Dimensional Gene Set
propagateGO: Propagate Gene Ontology annotation.
pval2index: Transform p-values in into a ranking index.
revList: Revert an annotation list.
splitOntologies: Split an annotation list of GO terms by ontologies.
transferIndex: Transfer a ranking index from regulatory elements, such as...
uvGsa: Uni-Variate Gene Set Analysis.
uvPat: Uni-Variate Gene Set Analysis Pattern Classification.
uvSignif: Filter significant terms in the univariate gene set analysis.

Functions

annot.size.filter Source code
annotFilter Man page Source code
annotList2mat Man page Source code
annotMat2list Man page Source code
getGOnames Man page Source code
getKEGGnames Man page Source code
getOntology Man page Source code
goLeaves Man page Source code
index.normalize Source code
index.standardize Source code
indexTransform Man page Source code
mdGsa Man page Source code
mdPat Man page Source code
multidimensionalGsa Man page
multivariateGsa Man page
plotMdGsa Man page Source code
propagateGO Man page Source code
propagateGO.matrix Source code
pval2index Man page Source code
revList Man page Source code
splitOntologies Man page Source code
transferIndex Man page Source code
univariateGsa Man page
uvGsa Man page Source code
uvPat Man page Source code
uvSignif Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS.md
R
R/annotFilter.R
R/annot_format.R
R/getOntology.R
R/get_GO_KEGG_names.R
R/goLeaves.R
R/indexTransform.R
R/mdGsa.R
R/mdPat.R
R/plotMdGsa.R
R/propagateGO.R
R/pval2index.R
R/splitOntologies.R
R/transferIndex.R
R/uvGsa.R
R/uvPat.R
R/uvSignif.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/mdgsa_vignette.R
inst/doc/mdgsa_vignette.Rmd
inst/doc/mdgsa_vignette.pdf
inst/extdata
inst/extdata/mdGsaPatterns.txt
inst/unitTests
inst/unitTests/test_IndexTransform.R
inst/unitTests/test_annotFilter.R
inst/unitTests/test_annot_format.R
inst/unitTests/test_getOntology.R
inst/unitTests/test_get_GO_KEGG_names.R
inst/unitTests/test_goLeaves.R
inst/unitTests/test_mdGsa.R
inst/unitTests/test_mdPat.R
inst/unitTests/test_propagateGO.R
inst/unitTests/test_pval2index.R
inst/unitTests/test_splitOntologies.R
inst/unitTests/test_transferIndex.R
inst/unitTests/test_uvGsa.R
inst/unitTests/test_uvPat.R
inst/unitTests/test_uvSignif.R
man
man/annotFilter.Rd
man/annotList2mat.Rd
man/annotMat2list.Rd
man/getGOnames.Rd
man/getKEGGnames.Rd
man/getOntology.Rd
man/goLeaves.Rd
man/indexTransform.Rd
man/mdGsa.Rd
man/mdPat.Rd
man/plotMdGsa.Rd
man/propagateGO.Rd
man/pval2index.Rd
man/revList.Rd
man/splitOntologies.Rd
man/transferIndex.Rd
man/uvGsa.Rd
man/uvPat.Rd
man/uvSignif.Rd
tests
tests/runTests.R
vignettes
vignettes/mdgsa_vignette.Rmd
mdgsa documentation built on May 20, 2017, 10:26 p.m.