mvGST Other Functions

Description

Internal functions used by the main functions of mvGST (graphCell, profileTable, go2GeneSets, pickOut, and p.adjust.SFL):

changeTO10 changes p-values in matrix to -1, 0, or 1, indicating significance.
combinePvalues Uses Stouffer's method to combine p-values in gene sets
convertPvalues converts p-values from one-sided to two-sided and vice versa
cut cuts out any all 0 rows from the matrix of results
fillInList fills in list of gene sets, ensuring that any gene in a child set is also in the parent set
finalResults counts the number of gene sets corresponding to each profile and contrast and creates results.table
geneNameConvertRows handles one-to-many and many-to-one problems of gene name translation
generateGeneSets creates list of gene sets
go2GeneSet creates a single matrix showing which profile a gene set fits into for each contrast tested
hartung Combines a set of p-values using Hartung's modified inverse normal method
interactiveGraph Creates a GO Graph of selected GO terms
method2 Uses Hartung's method to combine p-values and handles many-to-one problem of gene name translation
method3 Handles one-to-many problem of gene name translation by eliminating all but one of the many
method4 Combines method2 and method3
mvGSTObject Creates an mvGST object
mvSort Sorts results.table by row totals
oneSideBYAdjust Convert p-values to two-sided, then uses Benjamini-Yekutieli adjustment, and converts back to one-sided
print.mvGST prints the results.table in a clean way
print.summary.mvGST prints the summary of an mvGST object
profileCombine Determines profiles of each gene set at each contrast
profiles Defines the possible profiles
separate splits genes (and their p-values) into gene sets
summary.mvGST creates a summary of an mvGST object
tableColumns Creates the column names for the results.table
distributeWeight helper function for p.adjust.SFL
getCurrentChildren helper function for p.adjust.SFL
makeCoherent helper function for p.adjust.SFL
getAncestorsAndOffspring helper function for p.adjust.SFL
turnListAround From globaltest package, helper function for p.adjust.SFL

Details

To access the tutorial document for this package, type in R: vignette("mvGST")

Author(s)

John R. Stevens, Dennis S. Mecham, Garrett Saunders

References

Stevens, J. R., and Isom, S. C., 2012. "Gene set testing to characterize multivariately differentially expressed genes." Conference on Applied Statistics in Agriculture Proceedings, 24, pp. 125-137.

Mecham, D. S. (2014) "mvGST: Multivariate and Directional Gene Set Testing". MS Project, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/gradreports/382/

Saunders, G., 2014. "Family-wise error rate control in QTL mapping and gene ontology graphs with remarks on family selection." PhD thesis, Utah State University, Department of Mathematics and Statistics. http://digitalcommons.usu.edu/etd/2164/