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| 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.colGxEunstruct | 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 |