SNPs-Based Whole Genome Association Studies

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Documentation for package ‘SNPassoc’ version 2.1-0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

$<-.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'