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.

Author
Juan R Gonzlez, Llus Armengol, Elisabet Guin, Xavier Sol, and Vctor Moreno
Date of publication
2014-04-23 09:27:48
Maintainer
Juan R Gonzlez <jrgonzalez@creal.cat>
License
GPL (>= 2)
Version
1.9-2
URLs

View on CRAN

Man pages

association
Association analysis between a single SNP and a given...
BonferroniSig
Bonferroni correction of p values
GenomicControl
Population substructure
getSignificantSNPs
Extract significant SNPs from an object of class...
haplointeraction
Haplotype interaction with a covariate
HapMap
SNPs from HapMap project
inheritance
Collapsing (or recoding) genotypes into different categories...
int
Identify interaction term
interactionPval
Two-dimensional SNP analysis for association studies
intervals
Print ORs and 95% confidence intervals for an object of class...
isMonomorphic
Check whether a SNP is Monomorphic
LD
max-statistic for a 2x3 table
makegeno
Create a group of locus objects from some SNPs, assign to...
maxstat
max-statistic for a 2x3 table
odds
Extract odds ratios, 95% CI and pvalues
permTest
Permutation test analysis
plotMissing
Plot of missing genotypes
plotWGassociation
Function to plot -log p values from an object of class...
qqpval
Functions for inspecting population substructure
scanWGassociation
Whole genome association analysis
setupSNP
Convert columns in a dataframe to class 'snp'
snp
SNP object
SNPassoc-internal
Internal SNPstat functions
SNPs
SNPs in a case-control study
sortSNPs
Sort a vector of SNPs by genomic position
tableHWE
Test for Hardy-Weinberg Equilibrium
Tablemeanse
Descriptive sample size, mean, and standard error
TableNPer
Descriptive sample size and percentage
WGassociation
Whole genome association analysis

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