mdgsa: Multi Dimensional Gene Set Analysis.

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

Author
David Montaner <dmontaner@cipf.es>
Date of publication
None
Maintainer
David Montaner <dmontaner@cipf.es>
License
GPL
Version
1.6.0
URLs

View on Bioconductor

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.

Files in this package

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