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.

Author
Holger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski
Date of publication
None
Maintainer
Holger Schwender <holger.schw@gmx.de>
License
LGPL-2
Version
3.12.0

View on Bioconductor

Man pages

allelicTDT
Allelic TDT
colEMlrt
EM Likelihood Ratio Test
colGxE
Genotypic TDT for Gene-Environment Interactions
colGxGPerms
Permutation-Based gTDT for Two-Way Interactions
colPOlrt
Parent-of-Origin Tests
colTDTmaxTest
Maximum Genotypic TDT
colTDTsam
SAM and EBAM for Trio Data
findLDblocks
Identifying LD blocks
getLD
Computation of LD Measures
getMatPseudo
Generates Case-Pseudo-Control Matrix
lrControl
Control Parameters for Trio Logic Regression
ped2geno
Transformation of Ped-File
plot.getLD
Plotting a getLD or getLDlarge Object
plot.LDblocks
Plotting a LDblock Object
plot.trioLR
Plotting for trioLR Objects
poly4root
Roots of a Fourth Degree Polynomial
print.colGxE
Printing and Storing of colGxE objects
print.trioFS
Printing and plotting of a trioFS object
print.trioLR
Printing of trioLR Objects
probTDT
TDT on genotype probabilities matrix
read.pedfile
Reading a Ped File
removeSNPs
Remove SNPs or Trios
scoreTDT
Score Tests for SNPs, GxE, and GxG Interactions
tdt
Genotypic TDT
tdtGxG
Genotypic TDT for Two-Way Interactions
trio.check
Check Case-Parent Trio Data for Mendelian Errors
trio.data
Case-Parent Trio Data
trioFS
Trio Feature Selection
trioLR
Trio Logic Regression
trio.permTest
Permutation Tests for Trio Logic Regression
trio.power
Power and sample size calculation
trio.prepare
Generate Trio Data Format Suitable for Trio Logic Regression
trio.sim
Simulate Case-Parent Trios
vcf2geno
Transformation of VFC File

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