# An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

## Documentation for package ‘epistasisGA’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

case | SNP counts for the affected children of case-parent triads.
chrom.fitness.score | A function to assign a fitness score to a chromosome
combine.islands | A function to combine GADGETS results for individual islands into a single dataset.
compute.graphical.scores | A function to compute SNP-pair scores for network plots of results.
dad | SNP counts for the fathers of case-parent triads.
epistasis.test | A function to run a test of the null hypothesis that a collection of SNPs do not exhibit epistasis, conditional upon observed marginal SNP-disease associations.
epistasisGA | 'epistasisGA' package
GADGETS | A function to run the GADGETS method
global.test | A function to run a global test of the null hypothesis that there are no SNP-disease associations across a range of chromosome sizes
mom | SNP counts for the mothers of case-parent triads.
network.plot | A function to plot a network of SNPs with potential multi-SNP effects.
permute.dataset | A function to create permuted datasets for permutation based hypothesis testing.
preprocess.genetic.data | A function to pre-process case-parent triad of affected/unaffected sibling data.
run.gadgets | A function to run the GADGETS algorithm to detect multi-SNP effects in case-parent triad studies.
snp.annotations | RSID, REF, and ALT annotations for example dataset SNPs