mvGST.other {mvGST} | R Documentation

## 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/

[Package mvGST version 1.12.2 Index]