Package: SNPassoc 2.1-2

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>.

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

SNPassoc_2.1-2.tar.gz
SNPassoc_2.1-2.zip(r-4.5)SNPassoc_2.1-2.zip(r-4.4)SNPassoc_2.1-1.zip(r-4.3)
SNPassoc_2.1-2.tgz(r-4.4-any)SNPassoc_2.1-1.tgz(r-4.3-any)
SNPassoc_2.1-2.tar.gz(r-4.5-noble)SNPassoc_2.1-2.tar.gz(r-4.4-noble)
SNPassoc_2.1-2.tgz(r-4.4-emscripten)SNPassoc_2.1-1.tgz(r-4.3-emscripten)
SNPassoc.pdf |SNPassoc.html✨
SNPassoc/json (API)

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

Peer review:

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

Datasets:

On CRAN:

7.82 score 15 stars 6 packages 94 scripts 1.3k downloads 36 exports 88 dependencies

Last updated 15 days agofrom:49d93ae833. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winNOTEOct 29 2024
R-4.4-macNOTEOct 29 2024
R-4.3-winNOTEAug 21 2024
R-4.3-macNOTEAug 21 2024

Exports:additiveassociationBonferroni.sigcodominantdominantGenomicControlgetGeneSymbolgetNiceTablegetSignificantSNPshaplo.interactionintinteractionPvalintervalsis.MonomorphicLDLDplotLDtablemake.genomaxstatoddsoverdominantpermTestplotMissingpvaluesqqpvalrecessiverelatedscanWGassociationsetupSNPsnpsortSNPsTable.mean.seTable.N.PertableHWEWGassociationWGstats

Dependencies:arsenalbackportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacecpp11data.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gluegridExtragtablehaplo.statshighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetpillarpkgconfigplyrpoisbinompolsplinepurrrquantregR6rappdirsRColorBrewerRcpprlangrmarkdownrmsrpartrstudioapisandwichsassscalesSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo

SNPassoc: an R package to perform whole genome association studies

Juan R. Gonzalez, Victor Moreno

Rendered fromSNPassoc.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-10-28
Started: 2017-08-31

Readme and manuals

Help Manual

Help pageTopics
Association analysis between a single SNP and a given phenotypeassociation print.snpOut
SNP data on asthma case-control studyasthma
Bonferroni correction of p valuesBonferroni.sig
Population substructureGenomicControl
Get gene symbol from a list of SNPsgetGeneSymbol
Get Latex outputgetNiceTable
Extract significant SNPs from an object of class 'WGassociation'getSignificantSNPs
Haplotype interaction with a covariatehaplo.interaction print.haploOut
SNPs from HapMap projectHapMap
SNPs from HapMap projectHapMap.SNPs.pos
Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritanceadditive codominant dominant geneticModel inheritance overdominant recessive
Identify interaction termint
Two-dimensional SNP analysis for association studiesinteractionPval 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 tableLD LD.setupSNP LD.snp LDplot LDtable
Create a group of locus objects from some SNPs, assign to 'model.matrix' class.make.geno
max-statistic for a 2x3 tablemaxstat maxstat.default maxstat.matrix maxstat.setupSNP maxstat.table print.maxstat
Extract odds ratios, 95% CI and pvaluesodds
Permutation test analysispermTest plot.permTest print.permTest
Function to plot -log p values from an object of class 'WGassociation'plot.WGassociation
Plot of missing genotypesplotMissing
Functions for inspecting population substructureqqpval
Get related samplesrelated
SNPs from HapMap projectresHapMap
Whole genome association analysisscanWGassociation
Convert columns in a dataframe to class 'snp'$<-.setupSNP labels.setupSNP plot.setupSNP setupSNP summary.setupSNP [.setupSNP [<-.setupSNP [[<-.setupSNP
SNP objectadditive.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 studySNPs
SNPs in a case-control studySNPs.info.pos
Sort a vector of SNPs by genomic positionsortSNPs
Descriptive sample size, mean, and standard errorTable.mean.se
Descriptive sample size and percentageTable.N.Per
Test for Hardy-Weinberg Equilibriumprint.tableHWE tableHWE
Whole genome association analysisadditive.WGassociation codominant.WGassociation dominant.WGassociation labels.WGassociation overdominant.WGassociation print.WGassociation pvalues pvalues.WGassociation recessive.WGassociation summary.WGassociation WGassociation WGstats [.WGassociation