| newFocus-package {newFocus} | R Documentation |
True Discovery Guarantee by Combining Partial Closed Testings
Description
Closed testing has been proved powerful for true discovery guarantee. The computation of closed testing is, however, quite burdensome. A general way to reduce computational complexity is to combine partial closed testings for some prespecified feature sets of interest. Partial closed testings are performed at Bonferroni-corrected alpha level to guarantee the lower bounds for the number of true discoveries in prespecified sets are simultaneously valid. For any post hoc chosen sets of interest, coherence property is used to get the lower bound. In this package, we implement closed testing with globaltest to calculate the lower bound for number of true discoveries, see Ningning Xu et.al (2021) <arXiv:2001.01541> for detailed description.
Details
The DESCRIPTION file:
| Package: | newFocus |
| Type: | Package |
| Title: | True Discovery Guarantee by Combining Partial Closed Testings |
| Version: | 1.1 |
| Date: | 2021-06-22 |
| Author: | Ningning Xu |
| Maintainer: | Ningning Xu <n.xu@lumc.nl> |
| Description: | Closed testing has been proved powerful for true discovery guarantee. The computation of closed testing is, however, quite burdensome. A general way to reduce computational complexity is to combine partial closed testings for some prespecified feature sets of interest. Partial closed testings are performed at Bonferroni-corrected alpha level to guarantee the lower bounds for the number of true discoveries in prespecified sets are simultaneously valid. For any post hoc chosen sets of interest, coherence property is used to get the lower bound. In this package, we implement closed testing with globaltest to calculate the lower bound for number of true discoveries, see Ningning Xu et.al (2021) <arXiv:2001.01541> for detailed description. |
| License: | GPL (>= 2) |
| Depends: | ctgt |
| NeedsCompilation: | no |
| Packaged: | 2021-06-22 09:50:32 UTC; nxu |
| Repository: | CRAN |
Index of help topics:
choosepath A set of focus set index
ctbab Closed testing with branch and bound
discov True discoveries
newFocus The new focus level procedure
newFocus-package True Discovery Guarantee by Combining Partial
Closed Testings
pick True discoveries for non-focus level node
For the GO (Gene Ontology) terms chosen as focus level nodes, newFocus function will return the minimum number of true discoveries. For GO terms that are non-focus level nodes, we use pick to count the number of true discoveries based on the result of newFocus.
Author(s)
Ningning Xu
Maintainer: Ningning Xu <n.xu@lumc.nl>
References
Ningning Xu, Aldo solari, Jelle Goeman, Clsoed testing with global test, with applications on metabolomics data, arXiv:2001.01541, https://arxiv.org/abs/2001.01541
Jelle J. Goeman, Sara A. van de Geer, Floor de Kort, Hans C. van Houwelingen, A global test for groups of genes: testing association with a clinical outcome, Bioinformatics, Volume 20, Issue 1, 1 January 2004, Pages 93-99, https://doi.org/10.1093/bioinformatics/btg382