survSNP - Power Calculations for SNP Studies with Censored Outcomes

Conduct asymptotic and empirical power and sample size calculations for Single-Nucleotide Polymorphism (SNP) association studies with right censored time to event outcomes.

Last updated 2 years ago

gslcpp

2.81 score 16 scripts 262 downloads

snplist - Tools to Create Gene Sets

A set of functions to create SQL tables of gene and SNP information and compose them into a SNP Set, for example to export to a PLINK set.

Last updated 3 years ago

cpp

2.56 score 18 scripts 207 downloads

groupedSurv - Efficient Estimation of Grouped Survival Models Using the Exact Likelihood Function

These 'Rcpp'-based functions compute the efficient score statistics for grouped time-to-event data (Prentice and Gloeckler, 1978), with the optional inclusion of baseline covariates. Functions for estimating the parameter of interest and nuisance parameters, including baseline hazards, using maximum likelihood are also provided. A parallel set of functions allow for the incorporation of family structure of related individuals (e.g., trios). Note that the current implementation of the frailty model (Ripatti and Palmgren, 2000) is sensitive to departures from model assumptions, and should be considered experimental. For these data, the exact proportional-hazards-model-based likelihood is computed by evaluating multiple variable integration. The integration is accomplished using the 'Cuba' library (Hahn, 2005), and the source files are included in this package. The maximization process is carried out using Brent's algorithm, with the C++ code file from John Burkardt and John Denker (Brent, 2002).

Last updated 1 years ago

cppopenmp

2.00 score 3 scripts 313 downloads

fastJT - Efficient Jonckheere-Terpstra Test Statistics

This 'Rcpp'-based package implements highly efficient functions for the calculation of the Jonckheere-Terpstra statistic. It can be used for a variety of applications, including feature selection in machine learning problems, or to conduct genome-wide association studies (GWAS) with multiple quantitative phenotypes. The code leverages 'OpenMP' directives for multi-core computing to reduce overall processing time.

Last updated 4 years ago

cppopenmp

2.00 score 8 scripts 238 downloads