Package: trio 3.45.2

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

trio_3.45.2.tar.gz
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trio.pdf |trio.html✨
trio/json (API)

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

Peer review:

Datasets:

On BioConductor:trio-3.45.2(bioc 3.21)trio-3.44.0(bioc 3.20)

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

snpgeneticvariabilitymicroarraygenetics

4.36 score 19 scripts 303 downloads 4 mentions 55 exports 12 dependencies

Last updated 1 months agofrom:e7425b1075. Checks:1 OK, 5 NOTE, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winNOTEJan 28 2025
R-4.5-macNOTEJan 28 2025
R-4.5-linuxNOTEJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winERRORJan 28 2025
R-4.3-macERRORJan 28 2025

Exports:allelicTDTcolEMlrtcolGxEcolGxEPermscolGxGcolGxGPermscolMAFtriocolNtrioscolPOlrtcolTATcolTDTcolTDT2waycolTDTebamcolTDTinter2waycolTDTmaxStatcolTDTmaxTestcolTDTsamcompPermTDT2wayfastGxGfastGxGrecfindLDblocksgetGxEstatsgetLDgetLDlargegetMatPseudogtdt.ebamgtdt.statlrControlntrios2Domntrios2RecorderSNPsped2genopoly4rootpoly4rootMatprobTDTqingEnvread.pedfileremoveSNPsremoveTriosscoreGxEscoreGxGscoreMaxStatscoreTDTsplitBlockstdttdt2waytdtGxGtrio.checktrio.permTesttrio.powertrio.preparetrio.simtrioFStrioLRvcf2geno

Dependencies:BiobaseBiocGenericsdata.tablegenericslatticeLogicRegMASSMatrixmulttestscrimesiggenessurvival

Trio Logic Regression and genotypic TDT

Rendered fromtrio.Rnwusingutils::Sweaveon Jan 28 2025.

Last update: 2014-02-20
Started: 2013-09-03

Readme and manuals

Help Manual

Help pageTopics
Allelic TDTallelicTDT print.aTDT
EM Likelihood Ratio TestcolEMlrt print.colEMlrt
Genotypic TDT for Gene-Environment InteractionscolGxE colGxEPerms
Permutation-Based gTDT for Two-Way InteractionscolGxGPerms compPermTDT2way
Frequency of Genotype CombinationscolNtrios
Parent-of-Origin TestscolPOlrt colTAT print.polrt print.tat
Maximum Genotypic TDTcolTDTmaxStat colTDTmaxTest print.maxStatTrio print.maxTestTrio
SAM and EBAM for Trio DatacolTDTebam colTDTsam gtdt.ebam gtdt.stat
Identifying LD blocksfindLDblocks print.LDblock splitBlocks
Computation of LD MeasuresgetLD getLDlarge
Generates Case-Pseudo-Control MatrixgetMatPseudo
Control Parameters for Trio Logic RegressionlrControl
Frequency of Dominant or Recessive Genotype Combinationsntrios2Dom ntrios2Rec
Transformation of Ped-Fileped2geno
Plotting a getLD or getLDlarge Objectplot.getLD plot.getLDlarge
Plotting a LDblock Objectplot.LDblocks
Plotting for trioLR Objectsplot.trioLR
Roots of a Fourth Degree Polynomialpoly4root poly4rootMat
Printing and Storing of colGxE objectsgetGxEstats print.colGxE print.colGxEunstruct
Printing and plotting of a trioFS objectplot.trioFS print.trioFS
Printing of trioLR Objectsprint.trioLR
TDT on genotype probabilities matrixprobTDT
Reading a Ped Fileread.pedfile
Remove SNPs or TrioscolMAFtrio orderSNPs removeSNPs removeTrios
Score Tests for SNPs, GxE, and GxG Interactionsprint.maxScoreTrio print.scoreGxE print.scoreTDT scoreGxE scoreGxG scoreMaxStat scoreTDT
Genotypic TDTcolTDT print.colTDT print.tdt tdt
Genotypic TDT for Two-Way InteractionscolGxG colTDT2way colTDTinter2way fastGxG fastGxGrec print.colTDTepi print.tdtEpi tdt2way tdtGxG
Check Case-Parent Trio Data for Mendelian Errorstrio.check
Case-Parent Trio Datafreq.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 Regressiontrio.permTest
Power and sample size calculationprint.trio.power trio.power
Generate Trio Data Format Suitable for Trio Logic RegressionqingEnv trio.prepare
Simulate Case-Parent Triostrio.sim
Trio Feature SelectiontrioFS trioFS.default trioFS.formula trioFS.trioPrepare
Trio Logic RegressiontrioLR trioLR.default trioLR.formula trioLR.trioPrepare
Transformation of VFC Filevcf2geno