# SNPs-Based Whole Genome Association Studies

## Documentation for package ‘SNPassoc’ version 2.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A B C D G H I L M N O P Q R S T W misc

## -- A --

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

## -- B --

Bonferroni.sig | Bonferroni correction of p values

## -- C --

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

## -- D --

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

## -- G --

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'
Ginv | Compute Generalized Inverse of Input Matrix

## -- H --

haplo.em | EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control | Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.glm | GLM Regression of Trait on Ambiguous Haplotypes
haplo.glm.control | Create list of control parameters for haplo.glm
haplo.interaction | Haplotype interaction with a covariate
haplo.model.frame | Sets up a model frame for haplo.glm
haplo.score | Score Statistics for Association of Traits with Haplotypes
haplo.score.slide | Score Statistics for Association of Traits with Haplotypes
HapMap | SNPs from HapMap project
HapMap.SNPs.pos | SNPs from HapMap project
hla.demo | HLA Loci and Serologic Response to Measles Vaccination

## -- I --

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

## -- L --

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
louis.info | Louis Information for haplo.glm

## -- M --

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

## -- N --

na.geno.keep | Remove rows with NA in covariates, but keep genotypes with NAs

## -- O --

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

## -- P --

permTest | Permutation test analysis
plot.haplo.score | Plot Haplotype Frequencies versus Haplotype Score Statistics
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.haplo.glm | GLM Regression of Trait on Ambiguous Haplotypes
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
printBanner | Print a nice banner
pvalues | Whole genome association analysis
pvalues.WGassociation | Whole genome association analysis

## -- Q --

qqpval | Functions for inspecting population substructure

## -- R --

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

## -- S --

scanWGassociation | Whole genome association analysis
score.sim.control | Create the list of control parameters for simulations in haplo.score
setupGeno | Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
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

## -- T --

Table.mean.se | Descriptive sample size, mean, and standard error
Table.N.Per | Descriptive sample size and percentage
tableHWE | Test for Hardy-Weinberg Equilibrium

## -- W --

WGassociation | Whole genome association analysis
WGstats | Whole genome association analysis

## -- misc --

$<-.setupSNP | Convert columns in a dataframe to class 'snp'
[.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'