Package: SNPassoc 2.3.1

Dolors Pelegri

SNPassoc: SNPs-Based Whole Genome Association Studies

Functions to perform most of the common analysis in genome association studies are implemented. 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. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi:10.1093/bioinformatics/btm025>. This version includes internal copies of functions from the archived 'haplo.stats' package to maintain functionality.

Authors:Victor Moreno [aut], Juan R Gonzalez [aut], Dolors Pelegri [aut, cre]

SNPassoc_2.3.1.tar.gz
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SNPassoc_2.3.1.tgz(r-4.6-x86_64)SNPassoc_2.3.1.tgz(r-4.6-arm64)SNPassoc_2.3.1.tgz(r-4.5-x86_64)SNPassoc_2.3.1.tgz(r-4.5-arm64)
SNPassoc_2.3.1.tar.gz(r-4.7-arm64)SNPassoc_2.3.1.tar.gz(r-4.7-x86_64)SNPassoc_2.3.1.tar.gz(r-4.6-arm64)SNPassoc_2.3.1.tar.gz(r-4.6-x86_64)
SNPassoc_2.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SNPassoc/json (API)

# Install 'SNPassoc' in R:

install.packages('SNPassoc', repos = c('https://isglobal-brge.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/isglobal-brge/snpassoc/issues

Datasets:

asthma - SNP data on asthma case-control study
HapMap - SNPs from HapMap project
HapMap.SNPs.pos - SNPs from HapMap project
hla.demo - HLA Loci and Serologic Response to Measles Vaccination
resHapMap - SNPs from HapMap project
SNPs - SNPs in a case-control study
SNPs.info.pos - SNPs in a case-control study

On CRAN:

7.60 score 16 stars 100 scripts 1.3k downloads 132 mentions 48 exports 83 dependencies

Last updated from:f447edc118. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	279
linux-devel-x86_64	OK	297
source / vignettes	OK	339
linux-release-arm64	OK	259
linux-release-x86_64	OK	307
macos-release-arm64	OK	218
macos-release-x86_64	OK	326
macos-oldrel-arm64	OK	299
macos-oldrel-x86_64	OK	578
windows-devel	OK	230
windows-release	OK	207
windows-oldrel	OK	205
wasm-release	OK	256

Exports:additive association Bonferroni.sig codominant dominant GenomicControl getGeneSymbol getNiceTable getSignificantSNPs Ginv haplo.em haplo.glm haplo.glm.control haplo.interaction haplo.model.frame haplo.score haplo.score.slide int interactionPval intervals is.Monomorphic LD LDplot LDtable louis.info make.geno maxstat na.geno.keep odds overdominant permTest plotMissing printBanner pvalues qqpval recessive related scanWGassociation score.sim.control setupGeno setupSNP snp sortSNPs Table.mean.se Table.N.Per tableHWE WGassociation WGstats

Dependencies:backports base64enc bslib cachem checkmate cli cluster codetools colorspace cpp11 data.table digest dplyr evaluate farver fastmap fontawesome foreign Formula fs generics ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix MatrixModels memoise mime multcomp mvtnorm nlme nnet pillar pkgconfig plyr poisbinom polspline purrr quantreg R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rms rpart rstudioapi S7 sandwich sass scales SparseM stringi stringr survival TH.data tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml zoo

SNPassoc: an R package to perform whole genome association studies

Rendered fromSNPassoc.Rmdusingknitr::rmarkdown

Last update: 2026-03-24
Started: 2017-08-31

Help page	Topics
Association analysis between a single SNP and a given phenotype	association print.snpOut
SNP data on asthma case-control study	asthma
Bonferroni correction of p values	Bonferroni.sig
Population substructure	GenomicControl
Get gene symbol from a list of SNPs	getGeneSymbol
Get Latex output	getNiceTable
Extract significant SNPs from an object of class 'WGassociation'	getSignificantSNPs
Compute Generalized Inverse of Input Matrix	Ginv
EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci	haplo.em
Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci	haplo.em.control
GLM Regression of Trait on Ambiguous Haplotypes	haplo.glm print.haplo.glm
Create list of control parameters for haplo.glm	haplo.glm.control
Haplotype interaction with a covariate	haplo.interaction print.haploOut
Sets up a model frame for haplo.glm	haplo.model.frame
Score Statistics for Association of Traits with Haplotypes	haplo.score
Score Statistics for Association of Traits with Haplotypes	haplo.score.slide
SNPs from HapMap project	HapMap
SNPs from HapMap project	HapMap.SNPs.pos
HLA Loci and Serologic Response to Measles Vaccination	hla.demo
Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance	additive codominant dominant geneticModel inheritance overdominant recessive
Identify interaction term	int
Two-dimensional SNP analysis for association studies	interactionPval plot.SNPinteraction print.SNPinteraction
Print ORs and 95% confidence intervals for an object of class 'haplo.glm'	intervals intervals.haplo.glm print.intervals summary.haplo.glm
max-statistic for a 2x3 table	LD LD.setupSNP LD.snp LDplot LDtable
Louis Information for haplo.glm	louis.info
Create a group of locus objects from some SNPs, assign to 'model.matrix' class.	make.geno
max-statistic for a 2x3 table	maxstat maxstat.default maxstat.matrix maxstat.setupSNP maxstat.table print.maxstat
Remove rows with NA in covariates, but keep genotypes with NAs	na.geno.keep
Extract odds ratios, 95% CI and pvalues	odds
Permutation test analysis	permTest plot.permTest print.permTest
Plot Haplotype Frequencies versus Haplotype Score Statistics	plot.haplo.score
Function to plot -log p values from an object of class 'WGassociation'	plot.WGassociation
Plot of missing genotypes	plotMissing
Print a nice banner	printBanner
Functions for inspecting population substructure	qqpval
Get related samples	related
SNPs from HapMap project	resHapMap
Whole genome association analysis	scanWGassociation
Create the list of control parameters for simulations in haplo.score	score.sim.control
Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.	setupGeno
Convert columns in a dataframe to class 'snp'	$<-.setupSNP labels.setupSNP plot.setupSNP setupSNP summary.setupSNP [.setupSNP [<-.setupSNP [[<-.setupSNP
SNP object	additive.snp as.snp codominant.snp dominant.snp is.snp plot.snp print.snp print.summary.snp recessive.snp reorder.snp snp summary.snp [.snp
SNPs in a case-control study	SNPs
SNPs in a case-control study	SNPs.info.pos
Sort a vector of SNPs by genomic position	sortSNPs
Descriptive sample size, mean, and standard error	Table.mean.se
Descriptive sample size and percentage	Table.N.Per
Test for Hardy-Weinberg Equilibrium	print.tableHWE tableHWE
Whole genome association analysis	additive.WGassociation codominant.WGassociation dominant.WGassociation labels.WGassociation overdominant.WGassociation print.WGassociation pvalues pvalues.WGassociation recessive.WGassociation summary.WGassociation WGassociation WGstats [.WGassociation

Package: SNPassoc 2.3.1

SNPassoc: SNPs-Based Whole Genome Association Studies

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