Genome-Wide Haplotyping
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Documentation for package ‘GHap’ version 3.0.0
Help Pages
| 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 |