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SNPassoc (version 1.5-6)

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

1,899

Version

1.5-6

License

GPL version 2 or newer

Maintainer

Juan Gonzalez

Last Published

December 14th, 2022

Functions in SNPassoc (1.5-6)

setupSNP

Convert columns in a dataframe to class 'snp'
HapMap

SNPs from HapMap project
GenomicControl

Population substructure
int

Identify interaction term
haplo.interaction

Haplotype interaction with a covariate
plot.WGassociation

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

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

max-statistic for a 2x3 table
sortSNPs

Sort a vector of SNPs by genomic position
Table.mean.se

Descriptive sample size, mean, and standard error
SNPassoc-internal

Internal SNPstat functions
snp

SNP object
odds

Extract odds ratios, 95% CI and pvalues
maxstat

max-statistic for a 2x3 table
SNPs

SNPs in a case-control study
getSignificantSNPs

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

Permutation test analysis
inheritance

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

Whole genome association analysis
WGassociation

Whole genome association analysis
plotMissing

Plot of missing genotypes
is.Monomorphic

Check whether a SNP is Monomorphic
interactionPval

Two-dimensional SNP analysis for association studies
Table.N.Per

Descriptive sample size and percentage
Bonferroni.sig

Bonferroni correction of p values
association

Association analysis between a single SNP and a given phenotype
tableHWE

Test for Hardy-Weinberg Equilibrium
qqpval

Functions for inspecting population substructure
intervals

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