Package: trio 3.51.0

Holger Schwender

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.

Authors:Holger Schwender, Qing Li, Philipp Berger, Christoph Neumann, Margaret Taub, Ingo Ruczinski

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trio_3.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
trio/json (API)

# Install 'trio' in R:

install.packages('trio', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

freq.hap - Case-Parent Trio Data
LDdata - Case-Parent Trio Data
mat.test - Case-Parent Trio Data
prob.mat.test - Case-Parent Trio Data
simuBkMap - Case-Parent Trio Data
step3way - Case-Parent Trio Data
trio.gen.err - Case-Parent Trio Data
trio.gen1 - Case-Parent Trio Data
trio.gen2 - Case-Parent Trio Data
trio.ped.err - Case-Parent Trio Data
trio.ped1 - Case-Parent Trio Data
trio.ped2 - Case-Parent Trio Data

On BioConductor:trio-3.51.0(bioc 3.24)trio-3.50.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

snp geneticvariability microarray genetics

4.53 score 28 scripts 4 mentions 58 exports 12 dependencies

Last updated from:bbc40abba1. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	182
linux-devel-x86_64	NOTE	264
source / vignettes	OK	246
linux-release-x86_64	NOTE	249
macos-release-arm64	NOTE	135
macos-oldrel-arm64	NOTE	114
windows-devel	NOTE	201
windows-release	NOTE	180
windows-oldrel	NOTE	195
wasm-release	OK	127

Exports:addRefAlt allelicTDT colEMlrt colGxE colGxEPerms colGxG colGxGPerms colMAFtrio colNtrios colPOlrt colTAT colTDT colTDT2way colTDTebam colTDTinter2way colTDTmaxStat colTDTmaxTest colTDTsam combineNtrios combineNtriosList compPermTDT2way fastGxG fastGxGrec findLDblocks getGxEstats getLD getLDlarge getMatPseudo gtdt.ebam gtdt.stat lrControl ntrios2Dom ntrios2Rec orderSNPs ped2geno poly4root poly4rootMat probTDT qingEnv read.pedfile removeSNPs removeTrios scoreGxE scoreGxG scoreMaxStat scoreTDT splitBlocks tdt tdt2way tdtGxG trio.check trio.permTest trio.power trio.prepare trio.sim trioFS trioLR vcf2geno

Dependencies:Biobase BiocGenerics data.table generics lattice LogicReg MASS Matrix multtest scrime siggenes survival

Trio Logic Regression and genotypic TDT

Rendered fromtrio.Rnwusingutils::Sweave

Last update: 2026-04-06
Started: 2013-09-03

Help page	Topics
Allelic TDT	allelicTDT print.aTDT
EM Likelihood Ratio Test	colEMlrt print.colEMlrt
Genotypic TDT for Gene-Environment Interactions	colGxE colGxEPerms
Permutation-Based gTDT for Two-Way Interactions	colGxGPerms compPermTDT2way
Frequency of Genotype Combinations	addRefAlt colNtrios print.tabNtrios
Parent-of-Origin Tests	colPOlrt colTAT print.polrt print.tat
Maximum Genotypic TDT	colTDTmaxStat colTDTmaxTest print.maxStatTrio print.maxTestTrio
SAM and EBAM for Trio Data	colTDTebam colTDTsam gtdt.ebam gtdt.stat
Combining Matrices with Frequencies of Genotype Combinations	combineNtrios combineNtriosList
Identifying LD blocks	findLDblocks print.LDblock splitBlocks
Computation of LD Measures	getLD getLDlarge
Generates Case-Pseudo-Control Matrix	getMatPseudo
Control Parameters for Trio Logic Regression	lrControl
Frequency of Dominant or Recessive Genotype Combinations	ntrios2Dom ntrios2Rec
Transformation of Ped-File	ped2geno
Plotting a getLD or getLDlarge Object	plot.getLD plot.getLDlarge
Plotting a LDblock Object	plot.LDblocks
Plotting for trioLR Objects	plot.trioLR
Roots of a Fourth Degree Polynomial	poly4root poly4rootMat
Printing and Storing of colGxE objects	getGxEstats print.colGxE print.colGxEunstruct
Printing and plotting of a trioFS object	plot.trioFS print.trioFS
Printing of trioLR Objects	print.trioLR
TDT on genotype probabilities matrix	probTDT
Reading a Ped File	read.pedfile
Remove SNPs or Trios	colMAFtrio orderSNPs removeSNPs removeTrios
Score Tests for SNPs, GxE, and GxG Interactions	print.maxScoreTrio print.scoreGxE print.scoreTDT scoreGxE scoreGxG scoreMaxStat scoreTDT
Genotypic TDT	colTDT print.colTDT print.tdt tdt
Genotypic TDT for Two-Way Interactions	colGxG colTDT2way colTDTinter2way fastGxG fastGxGrec print.colTDTepi print.tdtEpi tdt2way tdtGxG
Check Case-Parent Trio Data for Mendelian Errors	trio.check
Case-Parent Trio Data	freq.hap LDdata mat.test prob.mat.test simuBkMap step3way trio.data trio.gen.err trio.gen1 trio.gen2 trio.ped.err trio.ped1 trio.ped2
Permutation Tests for Trio Logic Regression	trio.permTest
Power and sample size calculation	print.trio.power trio.power
Generate Trio Data Format Suitable for Trio Logic Regression	qingEnv trio.prepare
Simulate Case-Parent Trios	trio.sim
Trio Feature Selection	trioFS trioFS.default trioFS.formula trioFS.trioPrepare
Trio Logic Regression	trioLR trioLR.default trioLR.formula trioLR.trioPrepare
Transformation of VFC File	vcf2geno

Package: trio 3.51.0

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

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