Package: Rsampletrees
Type: Package
Title: Sampletrees Input/Output Processing
Description: Contains functions that are useful for pre- and post-processing the tree output from the MCMC-based C++ program sampletrees. The program sampletrees is used to sample gene genealogies conditional on either phased or unphased SNP genotype data. More information about sampletrees can be found at http://stat.sfu.ca/statgen/research/sampletrees.html . Pre-processing tasks involve creating the settings file, the haplotype estimation files (if input data is genotype), and error checking the settings. Post-processing involves reading in the MCMC output from a run of sampletrees and computing summary statistics.
Version: 0.1
Date: 2014-08-01
Author: Kelly Burkett, Brad McNeney, Jinko Graham
Maintainer: Kelly Burkett <kburkett@uottawa.ca>
Depends: haplo.stats, ape
License: GPL-2
Packaged: 2015-02-02 18:50:40 UTC; kellyburkett
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-02-02 20:45:11
Package: SNPassoc
Version: 1.9-2
Date: 2014-Apr-22
Depends: R (>= 3.0.0), haplo.stats, survival, mvtnorm, parallel
Title: SNPs-based whole genome association studies
Author: Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno
Maintainer: Juan R González <jrgonzalez@creal.cat>
Description: This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.
License: GPL (>= 2)
URL: http://www.creal.cat/jrgonzalez/software.htm
Encoding: latin1
Packaged: 2014-04-23 06:38:07 UTC; jrgonzalez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-23 09:27:48
Package: BVS
Type: Package
Title: Bayesian Variant Selection: Bayesian Model Uncertainty
Techniques for Genetic Association Studies
Author: Melanie Quintana <maw27.wilson@gmail.com>
Maintainer: Melanie Quintana <maw27.wilson@gmail.com>
Description: The functions in this package focus on analyzing
case-control association studies involving a group of genetic
variants. In particular, we are interested in modeling the
outcome variable as a function of a multivariate genetic
profile using Bayesian model uncertainty and variable selection
techniques. The package incorporates functions to analyze data
sets involving common variants as well as extensions to model
rare variants via the Bayesian Risk Index (BRI) as well as
haplotypes. Finally, the package also allows the incorporation
of external biological information to inform the marginal
inclusion probabilities via the iBMU.
Version: 4.12.1
License: Unlimited
Depends: MASS, msm, haplo.stats, R (>= 2.14.0)
Packaged: 2012-08-09 16:25:49 UTC; maw27
Repository: CRAN
Date/Publication: 2012-08-09 17:07:48
Package: haplo.ccs
Type: Package
Title: Estimate Haplotype Relative Risks in Case-Control Data
Version: 1.3.1
Date: 2011-10-27
Author: Benjamin French and Thomas Lumley
Depends: R (>= 2.13.0), haplo.stats, survival
Maintainer: Benjamin French <bcfrench@upenn.edu>
Description: 'haplo.ccs' estimates haplotype and covariate relative
risks in case-control data by weighted logistic regression.
Diplotype probabilities, which are estimated by EM computation
with progressive insertion of loci, are utilized as weights.
License: GPL (>= 2)
Packaged: 2012-10-29 08:58:55 UTC; ripley
Repository: CRAN
Date/Publication: 2012-10-29 08:58:55
providing 
.