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SNPassoc (version 1.0-2)

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)

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Version

Install

install.packages('SNPassoc')

Monthly Downloads

1,476

Version

1.0-2

License

GPL version 2 or newer

Maintainer

Juan Gonzalez

Last Published

December 14th, 2022

Functions in SNPassoc (1.0-2)

Plot of missing genotypes

Descriptive sample size, mean, and standard error

SNPs from HapMap project

Association analysis between a single SNP and a given phenotype

Sort a vector of SNPs by genomic position

getSignificantSNPs

Extract significant SNPs from an object of class 'WGassociation'

Bonferroni correction of p values

Genomic position for selected SNPs

Convert columns in a dataframe to class 'snp'

haplo.interaction

Haplotype interaction with a covariate

Whole genome association analysis

Identify interaction term

Descriptive sample size and percentage

plot.WGassociation

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

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

SNPassoc-internal

Internal SNPstat functions

Test for Hardy-Weinberg Equilibrium

interactionPval

Two-dimensional SNP analysis for association studies

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

Collapsing genotypes into two categories depending on a given genetic mode of inheritance

Check whether a SNP is Monomorphic

SNPs in a case-control study