$<-.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 |
asthma |
SNP data on asthma case-control study |
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 |
getGeneSymbol |
Get gene symbol from a list of SNPs |
getNiceTable |
Get Latex output |
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 |
related |
Get related samples |
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' |