GBJ - Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies

Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ), Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests. The GBJ has been shown to outperform other tests in genetic association studies when signals are correlated and moderately sparse. Please see the vignette for a quickstart guide or Sun and Lin (2017) <arXiv:1710.02469> for more details.

Last updated 11 months ago

cpp

5.16 score 2 stars 3 dependents 32 scripts 355 downloads

csmGmm - Conditionally Symmetric Multidimensional Gaussian Mixture Model

Implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (2024, <doi:10.1080/01621459.2024.2422124>). The paper is accepted and published online (but not yet in print) in the Journal of the American Statistical Association as of Dec 1 2024.

Last updated 23 days ago

3.73 score 108 scripts

ICSKAT - Interval-Censored Sequence Kernel Association Test

Implements the Interval-Censored Sequence Kernel Association (ICSKAT) test for testing the association between interval-censored time-to-event outcomes and groups of single nucleotide polymorphisms (SNPs). Interval-censored time-to-event data occur when the event time is not known exactly but can be deduced to fall within a given interval. For example, some medical conditions like bone mineral density deficiency are generally only diagnosed at clinical visits. If a patient goes for clinical checkups yearly and is diagnosed at, say, age 30, then the onset of the deficiency is only known to fall between the date of their age 29 checkup and the date of the age 30 checkup. Interval-censored data include right- and left-censored data as special cases. This package also implements the interval-censored Burden test and the ICSKATO test, which is the optimal combination of the ICSKAT and Burden tests. Please see the vignette for a quickstart guide.

Last updated 3 years ago

cpp

2.48 score 1 dependents 3 scripts 186 downloads

reconstructKM - Reconstruct Individual-Level Data from Published KM Plots

Functions for reconstructing individual-level data (time, status, arm) from Kaplan-MEIER curves published in academic journals (e.g. NEJM, JCO, JAMA). The individual-level data can be used for re-analysis, meta-analysis, methodology development, etc. This package was used to generate the data for commentary such as Sun, Rich, & Wei (2018) <doi:10.1056/NEJMc1808567>. Please see the vignette for a quickstart guide.

Last updated 4 years ago

2.30 score 2 scripts 135 downloads

DBpower - Finite Sample Power Calculations for Detection Boundary Tests

Calculates lower bound on power, upper bound on power, and exact power (small sets only) for detection boundary tests (e.g. Berk-Jones, Generalized Berk-Jones, innovated Berk-Jones) used in set-based inference studies. These detection boundary tests are described in Sun et al., (2019) <doi:10.1080/01621459.2019.1660170>.

Last updated 3 years ago

2.00 score 2 scripts 146 downloads