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 |