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SNPassoc (version 1.5-3)

SNPs-based whole genome association studies

Description

This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.

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Version

Install

install.packages('SNPassoc')

Monthly Downloads

1,476

Version

1.5-3

License

GPL version 2 or newer

Maintainer

Juan Gonz�lez

Last Published

December 14th, 2022

Functions in SNPassoc (1.5-3)

plotMissing

Plot of missing genotypes
getSignificantSNPs

Extract significant SNPs from an object of class 'WGassociation'
int

Identify interaction term
make.geno

Create a group of locus objects from some SNPs, assign to 'model.matrix' class.
setupSNP

Convert columns in a dataframe to class 'snp'
GenomicControl

Population substructure
Table.mean.se

Descriptive sample size, mean, and standard error
snp

SNP object
intervals

Print ORs and 95% confidence intervals for an object of class 'haplo.glm'
is.Monomorphic

Check whether a SNP is Monomorphic
odds

Extract odds ratios, 95% CI and pvalues
SNPassoc-internal

Internal SNPstat functions
HapMap

SNPs from HapMap project
SNPs

SNPs in a case-control study
scanWGassociation

Whole genome association analysis
haplo.interaction

Haplotype interaction with a covariate
interactionPval

Two-dimensional SNP analysis for association studies
maxstat

max-statistic for a 2x3 table
association

Association analysis between a single SNP and a given phenotype
tableHWE

Test for Hardy-Weinberg Equilibrium
inheritance

Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance
qqpval

Functions for inspecting population substructure
permTest

Permutation test analysis
Bonferroni.sig

Bonferroni correction of p values
Table.N.Per

Descriptive sample size and percentage
WGassociation

Whole genome association analysis
sortSNPs

Sort a vector of SNPs by genomic position
LD

max-statistic for a 2x3 table
plot.WGassociation

Function to plot -log p values from an object of class 'WGassociation'