SNPassoc: SNPs-based whole genome association studies

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. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated.

AuthorJuan R Gonzlez, Llus Armengol, Elisabet Guin, Xavier Sol, and Vctor Moreno
Date of publication2014-04-23 09:27:48
MaintainerJuan R Gonzlez <jrgonzalez@creal.cat>
LicenseGPL (>= 2)
Version1.9-2
http://www.creal.cat/jrgonzalez/software.htm

View on CRAN

Man pages

Files in this package

SNPassoc
SNPassoc/inst
SNPassoc/inst/docs
SNPassoc/inst/docs/todo.txt
SNPassoc/inst/docs/changelog.txt
SNPassoc/NAMESPACE
SNPassoc/data
SNPassoc/data/SNPs.rda
SNPassoc/data/HapMap.rda
SNPassoc/R
SNPassoc/R/interleave.R SNPassoc/R/z[.setupSNP.R SNPassoc/R/crea.lab.R SNPassoc/R/intervals.haplo.glm.R SNPassoc/R/SNPHWE.R SNPassoc/R/tableHWE.R SNPassoc/R/print.WGassociation.R SNPassoc/R/table.corner.R SNPassoc/R/assoc.R SNPassoc/R/recessive.R SNPassoc/R/maxstat.matrix.R SNPassoc/R/z[.WGassociation.R SNPassoc/R/dominant.default.R SNPassoc/R/is.snp.R SNPassoc/R/reorder.snp.R SNPassoc/R/summary.setupSNP.R SNPassoc/R/modelTest.R SNPassoc/R/dscore.setupSNP.R SNPassoc/R/print.tableHWE.R SNPassoc/R/make.geno.R SNPassoc/R/z[[_-.setupSNP.R SNPassoc/R/codominant.default.R SNPassoc/R/codominant.R SNPassoc/R/z$.setupSNP.R SNPassoc/R/summary.WGassociation.R SNPassoc/R/overdominant.R SNPassoc/R/plotMissing.R SNPassoc/R/pvalTest.R SNPassoc/R/pvalues.R SNPassoc/R/LD.R SNPassoc/R/dscore.R SNPassoc/R/scanWGassociation.R SNPassoc/R/GenotypeRate.R SNPassoc/R/intervals.or.R SNPassoc/R/association.R
SNPassoc/R/odds.r
SNPassoc/R/Table.mean.se.R SNPassoc/R/plot.WGassociation.R SNPassoc/R/print.permTest.R SNPassoc/R/print.haploOut.R SNPassoc/R/labels.setupSNP.R SNPassoc/R/summary.haplo.glm.R SNPassoc/R/as.snp.R SNPassoc/R/int.R SNPassoc/R/labels.WGassociation.R SNPassoc/R/getSignificantSNPs.R SNPassoc/R/maxstat.setupSNP.R SNPassoc/R/codominant.WGassociation.R SNPassoc/R/print.SNPinteraction.R SNPassoc/R/print.maxstat.R SNPassoc/R/additive.snp.R SNPassoc/R/Table.N.Per.R SNPassoc/R/print.LD.R SNPassoc/R/print.summary.snp.R SNPassoc/R/dominant.R SNPassoc/R/extractPval.i.R SNPassoc/R/overdominant.WGassociation.R SNPassoc/R/sortSNPs.R SNPassoc/R/is.quantitative.R SNPassoc/R/overdominant.default.R SNPassoc/R/haplo.interaction.R SNPassoc/R/permTest.R SNPassoc/R/maxstat.table.R
SNPassoc/R/c.WGassociation.r
SNPassoc/R/maxstat.R SNPassoc/R/additive.WGassociation.R SNPassoc/R/summary.snp.R SNPassoc/R/togeno.R SNPassoc/R/plot.setupSNP.R SNPassoc/R/codominant.snp.R SNPassoc/R/GenomicControl.R SNPassoc/R/dominant.WGassociation.R SNPassoc/R/additive.default.R SNPassoc/R/dominant.snp.R SNPassoc/R/table.interaction.R SNPassoc/R/plot.permTest.R SNPassoc/R/expandsetupSNP.R SNPassoc/R/extractPval.R
SNPassoc/R/print.snp.r
SNPassoc/R/z[_-.setupSNP.R SNPassoc/R/trim.R SNPassoc/R/plot.SNPinteraction.R SNPassoc/R/print.intervals.R SNPassoc/R/Bonferroni.sig.R SNPassoc/R/overdominant.snp.R SNPassoc/R/print.snpOut.R SNPassoc/R/setupSNP.R SNPassoc/R/is.Monomorphic.R SNPassoc/R/recessive.default.R SNPassoc/R/WGassociation.R SNPassoc/R/WGstats.R SNPassoc/R/plot.snp.R SNPassoc/R/orderChromosome.R SNPassoc/R/interactionPval.R SNPassoc/R/additive.R SNPassoc/R/pvalues.WGassociation.R SNPassoc/R/intervals.R SNPassoc/R/snp.R
SNPassoc/R/haplo.inter.fit.R
SNPassoc/R/qqpval.r
SNPassoc/R/association.fit.R SNPassoc/R/dscore.default.R
SNPassoc/R/z[.snp.r
SNPassoc/R/intervals.dif.R SNPassoc/R/recessive.WGassociation.R SNPassoc/R/maxstat.default.R SNPassoc/R/recessive.snp.R
SNPassoc/MD5
SNPassoc/DESCRIPTION
SNPassoc/man
SNPassoc/man/LD.Rd SNPassoc/man/tableHWE.Rd SNPassoc/man/isMonomorphic.Rd SNPassoc/man/plotMissing.Rd SNPassoc/man/inheritance.Rd SNPassoc/man/association.Rd SNPassoc/man/permTest.Rd SNPassoc/man/WGassociation.Rd SNPassoc/man/int.Rd SNPassoc/man/SNPs.Rd SNPassoc/man/maxstat.Rd SNPassoc/man/setupSNP.Rd SNPassoc/man/odds.Rd SNPassoc/man/BonferroniSig.Rd SNPassoc/man/scanWGassociation.Rd SNPassoc/man/Tablemeanse.Rd SNPassoc/man/HapMap.Rd SNPassoc/man/haplointeraction.Rd SNPassoc/man/TableNPer.Rd SNPassoc/man/interactionPval.Rd SNPassoc/man/snp.Rd SNPassoc/man/GenomicControl.Rd SNPassoc/man/plotWGassociation.Rd SNPassoc/man/intervals.Rd SNPassoc/man/qqpval.Rd SNPassoc/man/sortSNPs.Rd SNPassoc/man/getSignificantSNPs.Rd SNPassoc/man/makegeno.Rd SNPassoc/man/SNPassoc-internal.Rd

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