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