SNPs-based whole genome association studies

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Documentation for package `SNPassoc' version 1.4-6

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additive Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
additive.snp SNP object
additive.WGassociation Whole genome association analysis
as.snp SNP object
association Association analysis between a single SNP and a given phenotype
Bonferroni.sig Bonferroni correction of p values
codominant Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
codominant.snp SNP object
codominant.WGassociation Whole genome association analysis
dominant Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
dominant.snp SNP object
dominant.WGassociation Whole genome association analysis
geneticModel Collapsing (or recoding) genotypes into different categories (generally two) 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 (or recoding) genotypes into different categories (generally two) 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
labels.setupSNP Convert columns in a dataframe to class 'snp'
labels.WGassociation Whole genome association analysis
make.geno Create a group of locus objects from some SNPs, assign to 'model.matrix' class.
overdominant Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
overdominant.WGassociation Whole genome association analysis
permTest Permutation test analysis
plot.permTest Permutation test analysis
plot.setupSNP Convert columns in a dataframe to class 'snp'
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.permTest Permutation test analysis
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
pvalues Whole genome association analysis
recessive Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
recessive.snp SNP object
recessive.WGassociation Whole genome association analysis
reorder.snp SNP object
resHapMap SNPs from HapMap project
scanWGassociation Whole genome association analysis
setupSNP Convert columns in a dataframe to class 'snp'
snp SNP object
SNPs SNPs in a case-control study
SNPs.info.pos SNPs in a case-control study
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
WGstats Whole genome association analysis
[.setupSNP Convert columns in a dataframe to class 'snp'
[.WGassociation Whole genome association analysis