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

Files in this package

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

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