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.

Install the latest version of this package by entering the following in R:
install.packages("SNPassoc")
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

Functions

additive Man page
additive.default Man page
additive.snp Man page
additive.WGassociation Man page
as.snp Man page
assoc Man page
association Man page
association.fit Man page
Bonferroni.sig Man page
codominant Man page
codominant.default Man page
codominant.snp Man page
codominant.WGassociation Man page
crea.lab Man page
dominant Man page
dominant.default Man page
dominant.snp Man page
dominant.WGassociation Man page
expandsetupSNP Man page
extractPval Man page
extractPval.i Man page
geneticModel Man page
GenomicControl Man page
GenotypeRate Man page
getSignificantSNPs Man page
haplo.interaction Man page
haplo.inter.fit Man page
HapMap Man page
HapMap.SNPs.pos Man page
inheritance Man page
int Man page
interactionPval Man page
interleave Man page
intervals Man page
intervals.dif Man page
intervals.haplo.glm Man page
intervals.or Man page
is.Monomorphic Man page
is.quantitative Man page
is.snp Man page
labels.setupSNP Man page
labels.WGassociation Man page
LD Man page
LDplot Man page
LD.setupSNP Man page
LD.snp Man page
LDtable Man page
make.geno Man page
maxstat Man page
maxstat.default Man page
maxstat.matrix Man page
maxstat.setupSNP Man page
maxstat.table Man page
modelTest Man page
odds Man page
orderChromosome Man page
overdominant Man page
overdominant.default Man page
overdominant.WGassociation Man page
permTest Man page
plotMissing Man page
plot.permTest Man page
plot.setupSNP Man page
plot.snp Man page
plot.SNPinteraction Man page
plot.WGassociation Man page
print.haploOut Man page
print.intervals Man page
print.maxstat Man page
print.permTest Man page
print.snp Man page
print.SNPinteraction Man page
print.snpOut Man page
print.summary.snp Man page
print.tableHWE Man page
print.WGassociation Man page
pvalTest Man page
pvalues Man page
pvalues.WGassociation Man page
qqpval Man page
recessive Man page
recessive.default Man page
recessive.snp Man page
recessive.WGassociation Man page
reorder.snp Man page
resHapMap Man page
scanWGassociation Man page
setupSNP Man page
[<-.setupSNP Man page
[.setupSNP Man page
[[<-.setupSNP Man page
$<-.setupSNP Man page
snp Man page
[.snp Man page
SNPassoc-internal Man page
SNPHWE Man page
SNPs Man page
SNPs.info.pos Man page
sortSNPs Man page
summary.haplo.glm Man page
summary.setupSNP Man page
summary.snp Man page
summary.WGassociation Man page
table.corner Man page
tableHWE Man page
table.interaction Man page
Table.mean.se Man page
Table.N.Per Man page
togeno Man page
trim Man page
WGassociation Man page
[.WGassociation Man page
WGstats Man page

Files

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

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