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| $<-.setupSNP | Convert columns in a dataframe to class 'snp' |
| 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 |
| GenomicControl | Population substructure |
| 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 |
| LD | max-statistic for a 2x3 table |
| LD.setupSNP | max-statistic for a 2x3 table |
| LD.snp | max-statistic for a 2x3 table |
| LDplot | max-statistic for a 2x3 table |
| LDtable | max-statistic for a 2x3 table |
| make.geno | Create a group of locus objects from some SNPs, assign to 'model.matrix' class. |
| maxstat | max-statistic for a 2x3 table |
| maxstat.default | max-statistic for a 2x3 table |
| maxstat.matrix | max-statistic for a 2x3 table |
| maxstat.setupSNP | max-statistic for a 2x3 table |
| maxstat.table | max-statistic for a 2x3 table |
| odds | Extract odds ratios, 95\% CI and pvalues |
| 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.maxstat | max-statistic for a 2x3 table |
| print.permTest | Permutation test analysis |
| print.snp | SNP object |
| print.SNPinteraction | Two-dimensional SNP analysis for association studies |
| print.snpOut | Association analysis between a single SNP and a given phenotype |
| print.summary.snp | SNP object |
| print.tableHWE | Test for Hardy-Weinberg Equilibrium |
| print.WGassociation | Whole genome association analysis |
| pvalues | Whole genome association analysis |
| pvalues.WGassociation | Whole genome association analysis |
| qqpval | Functions for inspecting population substructure |
| 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' |
| [.snp | SNP object |
| [.WGassociation | Whole genome association analysis |
| [<-.setupSNP | Convert columns in a dataframe to class 'snp' |
| [[<-.setupSNP | Convert columns in a dataframe to class 'snp' |