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.
- John R. Stevens and Dennis S. Mecham
- Date of publication
- John R. Stevens <email@example.com>
- Creates tables showing profiles of specific gene sets.
- Makes a GO graph highlighting the GO terms in the selected...
- mvGST Other Functions
- Multivariate and directional gene set testing
- mvGSTsamples: Sample objects for the mvGST package
- Short Focus Level adjustment
- Returns gene sets in a cell of the 'results.table'.
- Creates a table of significance profiles of gene sets from...
Files in this package