checkMarkers | Basic data quality checks for markers |
checkMarkers.default | Basic data quality checks for markers |
checkMendelian | Check Mendelian Errors |
checkMendelian.default | Check Mendelian Errors |
fbat | Family-Based Association Tests |
fbat.default | Family-Based Association Tests |
getFounders | Get founders' information |
missGFreq | Count frequencies of missing genotypes |
missGFreq.default | Count frequencies of missing genotypes |
pedAFreq | get allele frequencies |
pedAFreq.default | get allele frequencies |
pedFlagHomo | flag homo/heterozygotes |
pedFlagHomo.default | flag homo/heterozygotes |
pedGFreq | get genotype frequencies |
pedGFreq.default | get genotype frequencies |
pedHardyWeinberg | Test Hardy-Weinberg equilibrium for each marker based on parental data |
pedHardyWeinberg.default | 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 |