Package: trio 3.45.0
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:
trio_3.45.0.tar.gz
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trio_3.45.0.tgz(r-4.4-any)trio_3.45.0.tgz(r-4.3-any)
trio_3.45.0.tar.gz(r-4.5-noble)trio_3.45.0.tar.gz(r-4.4-noble)
trio_3.45.0.tgz(r-4.4-emscripten)trio_3.45.0.tgz(r-4.3-emscripten)
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')) |
- LDdata - Case-Parent Trio Data
- freq.hap - 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-3.45.0(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
Last updated 23 days agofrom:68d3fd965d. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | ERROR | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:allelicTDTcolEMlrtcolGxEcolGxEPermscolGxGcolGxGPermscolMAFtriocolPOlrtcolTATcolTDTcolTDT2waycolTDTebamcolTDTinter2waycolTDTmaxStatcolTDTmaxTestcolTDTsamcompPermTDT2wayfastGxGfastGxGrecfindLDblocksgetGxEstatsgetLDgetLDlargegetMatPseudogtdt.ebamgtdt.statlrControlorderSNPsped2genopoly4rootpoly4rootMatprobTDTqingEnvread.pedfileremoveSNPsremoveTriosscoreGxEscoreGxGscoreMaxStatscoreTDTsplitBlockstdttdt2waytdtGxGtrio.checktrio.permTesttrio.powertrio.preparetrio.simtrioFStrioLRvcf2geno
Dependencies:BiobaseBiocGenericsgenericslatticeLogicRegMASSMatrixmulttestscrimesiggenessurvival
Readme and manuals
Help Manual
| 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 |
| 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 |
| 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 |
| 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 |
