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SNPassoc  

SNPs-Based Whole Genome Association Studies
View on CRAN: Click here


Download and install SNPassoc package within the R console
Install from CRAN:
install.packages("SNPassoc")

Install from Github:
library("remotes")
install_github("cran/SNPassoc")

Install by package version:
library("remotes")
install_version("SNPassoc", "2.1-2")



Attach the package and use:
library("SNPassoc")
Maintained by
Dolors Pelegri
[Scholar Profile | Author Map]
First Published: 2006-09-29
Latest Update: 2022-12-14
Description:
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>.
How to cite:
Dolors Pelegri (2006). SNPassoc: SNPs-Based Whole Genome Association Studies. R package version 2.1-2, https://cran.r-project.org/web/packages/SNPassoc. Accessed 05 May. 2025.
Previous versions and publish date:
1.0-2 (2006-09-29 16:07), 1.1-0 (2006-11-10 13:37), 1.1-1 (2006-11-19 10:38), 1.3-0 (2006-11-30 12:04), 1.4-1 (2007-01-18 11:16), 1.4-2 (2007-01-21 20:22), 1.4-3 (2007-01-22 20:08), 1.4-4 (2007-03-20 10:54), 1.4-5 (2007-03-21 09:29), 1.4-6 (2007-03-23 11:51), 1.4-8 (2007-05-29 17:22), 1.4-9 (2007-10-16 09:25), 1.5-1 (2008-03-27 20:11), 1.5-2 (2008-04-22 12:37), 1.5-3 (2008-05-05 16:08), 1.5-6 (2009-02-06 13:32), 1.5-7 (2009-03-04 08:50), 1.5-8 (2009-03-09 12:32), 1.6-0 (2009-07-18 17:35), 1.8-1 (2011-11-22 13:19), 1.8-4 (2012-09-03 14:25), 1.8-5 (2012-12-17 10:16), 1.9-1 (2013-11-08 14:58), 1.9-2.1 (2020-08-19 16:11), 1.9-2 (2014-04-23 09:27), 2.0-0 (2020-09-07 18:10), 2.0-1 (2020-10-13 10:30), 2.0-2 (2020-11-11 00:00), 2.0-11 (2021-12-03 09:40), 2.0-12 (2022-08-20 23:50), 2.0-17 (2022-10-04 11:20), 2.0-18 (2022-11-15 22:10), 2.1-0 (2022-12-14 21:20)
Other packages that cited SNPassoc R package
View SNPassoc citation profile
Other R packages that SNPassoc depends, imports, suggests or enhances
Complete documentation for SNPassoc
Functions, R codes and Examples using the SNPassoc R package
Some associated functions: BonferroniSig . GenomicControl . HapMap.SNPs.pos . HapMap . LD . SNPassoc-internal . SNPs.info.pos . SNPs . TableNPer . Tablemeanse . WGassociation . association . asthma . getGeneSymbol . getNiceTable . getSignificantSNPs . haplointeraction . inheritance . int . interactionPval . intervals . isMonomorphic . makegeno . maxstat . odds . permTest . plotMissing . plotWGassociation . qqpval . related . resHapMap . scanWGassociation . setupSNP . snp . sortSNPs . tableHWE . 
Some associated R codes: Bonferroni.sig.R . GenomicControl.R . GenotypeRate.R . LD.R . SNPHWE.R . Table.N.Per.R . Table.mean.se.R . WGassociation.R . WGstats.R . additive.R . additive.WGassociation.R . additive.default.R . additive.snp.R . as.snp.R . assoc.R . association.R . association.fit.R . codominant.R . codominant.WGassociation.R . codominant.default.R . codominant.snp.R . crea.lab.R . dominant.R . dominant.WGassociation.R . dominant.default.R . dominant.snp.R . expandsetupSNP.R . extractPval.R . extractPval.i.R . getGeneSymbol.R . getNiceTable.R . getSignificantSNPs.R . haplo.inter.fit.R . haplo.interaction.R . int.R . interactionPval.R . interleave.R . intervals.R . intervals.dif.R . intervals.haplo.glm.R . intervals.or.R . is.Monomorphic.R . is.quantitative.R . is.snp.R . labels.WGassociation.R . labels.setupSNP.R . make.geno.R . maxstat.R . maxstat.default.R . maxstat.matrix.R . maxstat.setupSNP.R . maxstat.table.R . modelTest.R . orderChromosome.R . overdominant.R . overdominant.WGassociation.R . overdominant.default.R . overdominant.snp.R . permTest.R . plot.SNPinteraction.R . plot.permTest.R . plot.setupSNP.R . plot.snp.R . plotMissing.R . plotWGassociation.R . print.LD.R . print.SNPinteraction.R . print.WGassociation.R . print.haploOut.R . print.intervals.R . print.maxstat.R . print.permTest.R . print.snpOut.R . print.summary.snp.R . print.tableHWE.R . pvalTest.R . pvalues.R . pvalues.WGassociation.R . recessive.R . recessive.WGassociation.R . recessive.default.R . recessive.snp.R . related.R . reorder.snp.R . scanWGassociation.R . setupSNP.R . snp.R . sortSNPs.R . summary.WGassociation.R . summary.haplo.glm.R . summary.setupSNP.R . summary.snp.R . table.corner.R . table.interaction.R . tableHWE.R . togeno.R . trim.R . z$.setupSNP.R . z[.WGassociation.R . z[.setupSNP.R . z[[_-.setupSNP.R . z[_-.setupSNP.R .  Full SNPassoc package functions and examples
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