SNPs-based whole genome association studies

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Documentation for package ‘SNPassoc’ version 1.5-2

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A B C D G H I L M 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

-- 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
getSignificantSNPs Extract significant SNPs from an object of class 'WGassociation'

-- H --

haplo.interaction Haplotype interaction with a covariate
HapMap SNPs from HapMap project
HapMap.SNPs.pos SNPs from HapMap project

-- 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
LDplot max-statistic for a 2x3 table
LDtable max-statistic for a 2x3 table

-- M --

make.geno Create a group of locus objects from some SNPs, assign to 'model.matrix' class.
maxstat max-statistic for a 2x3 table

-- 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.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

-- 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
reorder.snp SNP object
resHapMap SNPs from HapMap project

-- S --

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

-- 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'
[.snp SNP object
[.WGassociation Whole genome association analysis