# Brad McNeney

#### 9 packages on CRAN

Exploratory tools to identify closely related subjects using autosomal genetic marker data.

Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. Users should note that the imported package 'snpStats' and the suggested packages 'rtracklayer', 'GenomicRanges', 'GenomInfoDb' and 'IRanges' are all BioConductor packages <https://bioconductor.org>.

R-interface to gene drop programs from Alun Thomas' Java Programs for Statistical Genetics and Computational Statistics (JPSGCS).

Implements a Markov Chain Monte Carlo algorithm to approximate exact conditional inference for logistic regression models. Exact conditional inference is based on the distribution of the sufficient statistics for the parameters of interest given the sufficient statistics for the remaining nuisance parameters. Using model formula notation, users specify a logistic model and model terms of interest for exact inference. See Zamar et al. (2007) <doi:10.18637/jss.v021.i03> for more details.

The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.

Likelihood inference in case-control studies of a rare disease under independence or simple dependence of genetic and non-genetic covariates

Sample ancestral trees conditional on phased or unphased SNP genotype data. The actual tree sampling is done using a C++ program that is launched within R. The package also contains functions for specifying the tree-sampling settings (pre-processing) and for storing and manipulating the sampled trees (post-processing). More information about 'sampletrees' can be found at <http://stat.sfu.ca/statgen/research/sampletrees.html>.

The package contains functions that 1) estimates gene-environment interaction between a SNP and a continuous non-genetic attribute by fitting a generalized additive model to case-parent trio data, 2) produces graphical displays of estimated interaction, 3) performs permutation test of gene-environment interaction; 4) simulates informative case-parent trios.