SNPs-Based Whole Genome Association Studies

Functions to perform most of the common analysis in genome association studies are implemented. 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. The methods are described in Gonzalez JR et al. (2007) .


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install.packages("SNPassoc")

2.0-2 by Juan R Gonzalez, 24 days ago


https://brge.isglobal.org


Browse source code at https://github.com/cran/SNPassoc


Authors: Juan R Gonzalez and Victor Moreno


Documentation:   PDF Manual  


Task views: Statistical Genetics, Missing Data


GPL (>= 2) license


Imports haplo.stats, mvtnorm, parallel, survival, tidyr, plyr, ggplot2, BiocStyle, poisbinom

Suggests testthat, knitr, rmarkdown, biomaRt


See at CRAN