anc2plink | Convert ancestry tracks to PLINK binary |
ancmark | Per marker ancestry proportions |
ancplot | Barplot of predictions of ancestry proportions |
ancsmooth | Smoothing of haplotype ancestry predictions |
ancsvm | SVM-based predictions of haplotype ancestry |
anctest | Prediction of haplotype ancestry |
anctrain | Construction of prototype alleles |
assoc | Genome-wide association analysis |
blockgen | Haplotype block generator |
blockstats | HapBlock statistics |
compress | Compress phased genotype data |
exfiles | Example files |
fast2phase | Convert fastPHASE data into the GHap phase format |
freq | Compute marker allele frequencies |
froh | Calculation of genomic inbreeding (FROH) |
fst | Haplotype-based Fst |
getHinv | Compute the inverse of H |
hap2plink | Convert haplotype allele counts to PLINK binary |
haplotyping | Haplotype genotypes |
hapstats | Haplotype allele statistics |
ibd | Estimation of IBD sharing |
inbcoef | Compute measures of inbreeding |
karyoplot | Individual chromosome painting |
kinship | Relationship matrix based on genomic data |
lmm | Linear mixed model |
loadhaplo | Load haplotype genotype data |
loadphase | Load binary phased genotype data |
loadplink | Load binary PLINK data |
makefile | Create example input files |
manhattan | Manhattan plot |
oxford2phase | Convert Oxford data into GHap phase |
pedcheck | Summary statistics for pedigree |
phase2plink | Export phase object to PLINK binary |
predictblup | Predict BLUP from reference |
profile | Genomic profile |
relfind | Find relatives in IBD estimates |
remlci | Confidence intervals for functions of variance components |
roh | Detection of runs of homozygosity (ROH) |
simadmix | Simulate individuals from specified admixture proportions |
simmating | Simulate individuals from specified matings |
simpheno | Quantitative trait simulation using real genotype data |
slice | Get a slice of a GHap object |
subset | Subset GHap objects |
varblup | Convert BLUP of individuals into BLUP of variants |
vcf2phase | Convert VCF data into GHap phase |
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