additive |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
as.snp |
SNP object |
association |
Association analysis between a single SNP and a given phenotype |
Bonferroni.sig |
Bonferroni correction of p values |
codominant |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
dominant |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
geneticModel |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
getSignificantSNPs |
Extract significant SNPs from an object of class 'WGassociation' |
haplo.interaction |
Haplotype interaction with a covariate |
HapMap |
SNPs from HapMap project |
HapMap.SNPs.pos |
SNPs from HapMap project |
inheritance |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
int |
Identify interaction term |
interactionPval |
Two-dimensional SNP analysis for association studies |
intervals |
Print ORs and 95% confidence intervals for an object of class 'haplo.glm' |
intervals.haplo.glm |
Print ORs and 95% confidence intervals for an object of class 'haplo.glm' |
is.snp |
SNP object |
make.geno |
Create a group of locus objects from some SNPs, assign to 'model.matrix' class. |
overdominant |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
plot.snp |
SNP object |
plot.SNPinteraction |
Two-dimensional SNP analysis for association studies |
plot.WGassociation |
Function to plot -log p values from an object of class 'WGassociation' |
plotMissing |
Plot of missing genotypes |
print.haploOut |
Haplotype interaction with a covariate |
print.intervals |
Print ORs and 95% confidence intervals for an object of class 'haplo.glm' |
print.SNPinteraction |
Two-dimensional SNP analysis for association studies |
print.snpOut |
Association analysis between a single SNP and a given phenotype |
print.tableHWE |
Test for Hardy-Weinberg Equilibrium |
print.WGassociation |
Whole genome association analysis |
recessive |
Collapsing genotypes into two categories depending on a given genetic mode of inheritance |
reorder.snp |
SNP object |
resHapMap |
SNPs from HapMap project |
setupSNP |
Convert columns in a dataframe to class 'snp' |
snp |
SNP object |
SNPs |
SNPs in a case-control study |
SNPs.info.pos |
Genomic position for selected SNPs |
sortSNPs |
Sort a vector of SNPs by genomic position |
summary.haplo.glm |
Print ORs and 95% confidence intervals for an object of class 'haplo.glm' |
summary.setupSNP |
Convert columns in a dataframe to class 'snp' |
summary.snp |
SNP object |
summary.WGassociation |
Whole genome association analysis |
Table.mean.se |
Descriptive sample size, mean, and standard error |
Table.N.Per |
Descriptive sample size and percentage |
tableHWE |
Test for Hardy-Weinberg Equilibrium |
WGassociation |
Whole genome association analysis |