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| checkMarkers | Basic data quality checks for markers |
| checkMendelian | Check Mendelian Errors |
| fbat | Family-Based Association Tests |
| getFounders | Get founders' information |
| missGFreq | Count frequencies of missing genotypes |
| pedAFreq | get allele frequencies |
| pedFlagHomo | flag homo/heterozygotes |
| pedGFreq | get genotype frequencies |
| pedHardyWeinberg | Test Hardy-Weinberg equilibrium for each marker based on parental data |
| readHapMap | Import HapMap data |
| readLink | Import file with PLINK data format |
| readPed | Import pedigree file from standard pedigree file format |
| sampleInfoCEU | Information about HapMap CEU subjects |
| sampleInfoCHB | Information about HapMap CHB subjects |
| sampleInfoJPT | Information about HapMap JPT subjects |
| sampleInfoYRI | Information about HapMap YRI subjects |
| summaryPvalue | summarize the test statistics and p-values |
| viewFlagHomo | flag homo/heterozygotes for specified marker |
| viewHW | View allele frequencies, Hardy-Weinberg equilibrium test statistics for specified marker |
| viewstat | view statistics for a marker |