mvGST.other: mvGST Other Functions
In johnrstevens/mvGST: Multivariate and directional gene set testing

Description Details Author(s) References

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

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

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

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. http://newprairiepress.org/agstatconference/2012/proceedings/10/

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/

johnrstevens/mvGST documentation built on May 7, 2019, 10:51 p.m.