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SNPassoc (version 1.1-1)

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

1.1-1

License

GPL version 2 or newer

Maintainer

Juan Gonzalez

Last Published

December 14th, 2022

Functions in SNPassoc (1.1-1)

make.geno

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

Whole genome association analysis
int

Identify interaction term
Bonferroni.sig

Bonferroni correction of p values
SNPassoc-internal

Internal SNPstat functions
SNPs.info.pos

Genomic position for selected SNPs
Table.N.Per

Descriptive sample size and percentage
inheritance

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

Association analysis between a single SNP and a given phenotype
plotMissing

Plot of missing genotypes
haplo.interaction

Haplotype interaction with a covariate
snp

SNP object
sortSNPs

Sort a vector of SNPs by genomic position
is.Monomorphic

Check whether a SNP is Monomorphic
plot.WGassociation

Function to plot -log p values from an object of class 'WGassociation'
Table.mean.se

Descriptive sample size, mean, and standard error
intervals

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

Statistics for an object of class 'WGassociation'
setupSNP

Convert columns in a dataframe to class 'snp'
HapMap

SNPs from HapMap project
scanWGassociation

Whole genome association analysis
getSignificantSNPs

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

Two-dimensional SNP analysis for association studies
tableHWE

Test for Hardy-Weinberg Equilibrium
SNPs

SNPs in a case-control study