trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

AuthorHolger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski
Date of publicationNone
MaintainerHolger Schwender <holger.schw@gmx.de>
LicenseLGPL-2
Version3.12.0

View on Bioconductor

Functions

allelicTDT Man page
colEMlrt Man page
colGxE Man page
colGxEPerms Man page
colGxG Man page
colGxGPerms Man page
colMAFtrio Man page
colPOlrt Man page
colTAT Man page
colTDT Man page
colTDT2way Man page
colTDTebam Man page
colTDTinter2way Man page
colTDTmaxStat Man page
colTDTmaxTest Man page
colTDTsam Man page
compPermTDT2way Man page
fastGxG Man page
fastGxGrec Man page
findLDblocks Man page
freq.hap Man page
getGxEstats Man page
getLD Man page
getLDlarge Man page
getMatPseudo Man page
gtdt.ebam Man page
gtdt.stat Man page
LDdata Man page
lrControl Man page
mat.test Man page
orderSNPs Man page
ped2geno Man page
plot.getLD Man page
plot.getLDlarge Man page
plot.LDblocks Man page
plot.trioFS Man page
plot.trioLR Man page
poly4root Man page
poly4rootMat Man page
print.aTDT Man page
print.colEMlrt Man page
print.colGxE Man page
print.colGxEunstruct Man page
print.colTDT Man page
print.colTDTepi Man page
print.LDblock Man page
print.maxScoreTrio Man page
print.maxStatTrio Man page
print.maxTestTrio Man page
print.polrt Man page
print.scoreGxE Man page
print.scoreTDT Man page
print.tat Man page
print.tdt Man page
print.tdtEpi Man page
print.trioFS Man page
print.trioLR Man page
print.trio.power Man page
prob.mat.test Man page
probTDT Man page
read.pedfile Man page
removeSNPs Man page
removeTrios Man page
scoreGxE Man page
scoreGxG Man page
scoreMaxStat Man page
scoreTDT Man page
simuBkMap Man page
splitBlocks Man page
step3way Man page
tdt Man page
tdt2way Man page
tdtGxG Man page
trio.check Man page
trio.data Man page
trioFS Man page
trioFS.default Man page
trioFS.formula Man page
trioFS.trioPrepare Man page
trio.gen1 Man page
trio.gen2 Man page
trio.gen.err Man page
trioLR Man page
trioLR.default Man page
trioLR.formula Man page
trioLR.trioPrepare Man page
trio.ped1 Man page
trio.ped2 Man page
trio.ped.err Man page
trio.permTest Man page
trio.power Man page
trio.prepare Man page
trio.sim Man page
vcf2geno Man page

Files

trio/DESCRIPTION
trio/NAMESPACE
trio/R
trio/R/allelicTDT.R trio/R/colEMlrt.R trio/R/colGxE.R trio/R/colGxEPerms.R trio/R/colGxGperm.R trio/R/colMAFtrio.R trio/R/colPOlrt.R trio/R/colTAT.R trio/R/colTDTmaxTest.R trio/R/colTDTsam.R trio/R/fastGxG.R trio/R/fastTDT.R trio/R/getLD.R trio/R/getLDlarge.R trio/R/lrControl.R trio/R/ped2geno.R trio/R/poly4root.R trio/R/probTDT.R trio/R/qingInternal.R trio/R/read.pedfile.R trio/R/removeSNPs.R trio/R/scoreTDT.R trio/R/splitBlocks.R trio/R/tdt.R trio/R/trio.R trio/R/trio.check.R trio/R/trio.permTest.R trio/R/trio.power.R trio/R/trio.sim.R trio/R/trioFS.R trio/R/trioLR.R trio/R/triologreg.R trio/R/vcf2geno.R trio/R/zzz.R
trio/build
trio/build/vignette.rds
trio/data
trio/data/trio.data.RData
trio/inst
trio/inst/doc
trio/inst/doc/trio.R
trio/inst/doc/trio.Rnw
trio/inst/doc/trio.pdf
trio/man
trio/man/allelicTDT.Rd trio/man/colEMlrt.Rd trio/man/colGxE.Rd trio/man/colGxGPerms.Rd trio/man/colPOlrt.Rd trio/man/colTDTmaxTest.Rd trio/man/colTDTsam.Rd trio/man/findLDblocks.Rd trio/man/getLD.Rd trio/man/getMatPseudo.Rd trio/man/lrControl.Rd trio/man/ped2geno.Rd trio/man/plot.LDblocks.Rd trio/man/plot.getLD.Rd trio/man/plot.trioLR.Rd trio/man/poly4root.Rd trio/man/print.colGxE.Rd trio/man/print.trioFS.Rd trio/man/print.trioLR.Rd trio/man/probTDT.Rd trio/man/read.pedfile.Rd trio/man/removeSNPs.Rd trio/man/scoreTDT.Rd trio/man/tdt.Rd trio/man/tdtGxG.Rd trio/man/trio.check.Rd trio/man/trio.data.Rd trio/man/trio.permTest.Rd trio/man/trio.power.Rd trio/man/trio.prepare.Rd trio/man/trio.sim.Rd trio/man/trioFS.Rd trio/man/trioLR.Rd trio/man/vcf2geno.Rd
trio/vignettes
trio/vignettes/figure1ld.eps
trio/vignettes/figure1ld.png
trio/vignettes/figure1lr.eps
trio/vignettes/figure1lr.png
trio/vignettes/figure2ld.eps
trio/vignettes/figure2ld.png
trio/vignettes/figure2lr.eps
trio/vignettes/figure2lr.png
trio/vignettes/figure3ld.eps
trio/vignettes/figure3ld.png
trio/vignettes/figure3lr.eps
trio/vignettes/figure3lr.png
trio/vignettes/qingSweave.sty
trio/vignettes/trio.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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