mvGST: Multivariate and directional gene set testing

mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.

Author
John R. Stevens and Dennis S. Mecham
Date of publication
None
Maintainer
John R. Stevens <john.r.stevens@usu.edu>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

go2Profile
Creates tables showing profiles of specific gene sets.
graphCell
Makes a GO graph highlighting the GO terms in the selected...
mvGST.other
mvGST Other Functions
mvGST-package
Multivariate and directional gene set testing
mvGSTsamples
mvGSTsamples: Sample objects for the mvGST package
p.adjust.SFL
Short Focus Level adjustment
pickOut
Returns gene sets in a cell of the 'results.table'.
profileTable
Creates a table of significance profiles of gene sets from...

Files in this package

mvGST/DESCRIPTION
mvGST/NAMESPACE
mvGST/NEWS
mvGST/R
mvGST/R/go2Profile.R
mvGST/R/graphCell.R
mvGST/R/mvGST.other.R
mvGST/R/p.adjust.SFL.R
mvGST/R/pickOut.R
mvGST/R/profileTable.R
mvGST/build
mvGST/build/vignette.rds
mvGST/data
mvGST/data/datalist
mvGST/data/mvGSTsamples.rda
mvGST/inst
mvGST/inst/doc
mvGST/inst/doc/mvGST.R
mvGST/inst/doc/mvGST.Rnw
mvGST/inst/doc/mvGST.pdf
mvGST/man
mvGST/man/go2Profile.Rd
mvGST/man/graphCell.Rd
mvGST/man/mvGST-package.Rd
mvGST/man/mvGST.other.Rd
mvGST/man/mvGSTsamples.Rd
mvGST/man/p.adjust.SFL.Rd
mvGST/man/pickOut.Rd
mvGST/man/profileTable.Rd
mvGST/vignettes
mvGST/vignettes/mvGST.Rnw