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

## Documentation for package ‘trio’ version 3.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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