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

## Documentation for package ‘epistasisGA’ version 1.6.0

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

## Help Pages

case | Genotypes for the affected children of case-parent triads.
case.gxe | Genotypes for the cases of case-parent triads with a simulated gene environment interaction.
case.mci | Genotypes for the affected cases of case-parent triads with a simulated maternal-fetal interaction.
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 | Genotypes for the fathers of case-parent triads.
dad.gxe | Genotypes for the fathers of case-parent triads with a simulated gene environment interaction.
dad.mci | Genotypes for the fathers of case-parent triads with a simulated maternal-fetal interaction.
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
exposure | Exposures for the cases of case-parent triads with a simulated gene environment interaction.
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
GxE.fitness.score | A function to assign an E-GADGETS (GxGxE) fitness score to a chromosome
GxE.test | A function to run a test of interaction between a collection of SNPs and exposures (experimental).
mom | Genotypes for the mothers of case-parent triads.
mom.gxe | Genotypes for the mothers of case-parent triads with a simulated gene environment interaction.
mom.mci | Genotypes for the mothers of case-parent triads with a simulated maternal-fetal interaction.
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 or disease-discordant 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
snp.annotations.mci | RSID, REF, and ALT annotations for example dataset SNPs