Man pages for GreenwoodLab/RVPedigree
Methods for Family-Based Rare-Variant Genetic Association Tests
| ASKAT.region | Run the ASKAT method on a genomic region defined by a start... |
| compute.weights | Compute/create matrix with genotype weights |
| Estim.H0.ASKAT | Estimation of the variance components under the null model... |
| Estim.H0.NormalizedASKAT | Estimation of the variance components under the null model... |
| Estim.H0.VCC | Estimate the model parameters under the null model |
| Get.G | Create genotypes from haplotypes |
| GetRelMatrix | Estimate relationship matrix based on pedigree or genomic... |
| Normality.test | Test for normality of the trait/phenotype |
| NormalizedASKAT.region | Run the normalized ASKAT method on a genomic region defined... |
| perm.hap | Permute haplotypes |
| Preparation.hap.perm | Prepare for the haplotype permutation |
| Preparation.VCC | Prepare for the VC-C methods |
| pvalue.ASKAT | Compute p-value and score for the ASKAT method |
| pvalue.NormalizedASKAT | Compute p-value and score for the normalized ASKAT method |
| pvalue.VCC1 | Compute score and p-value for the VC-C1 method |
| pvalue.VCC2 | Compute the p-value for the VC-C2 method |
| pvalue.VCC3 | Compute p-values for the VC-C3 method |
| read.haplo | Read haplotype data, selected by region of interest, from... |
| read.haplo.bedfile | Read haplotype data, selected by region of interest, from BED... |
| read.haplo.pedfile | Read haplotype data, selected by region of interest, from PED... |
| read.haplo.shapeit_haps | Read haplotype data, selected by region of interest, from a... |
| readMapFile | Read file with information about SNPs chromosome and... |
| read.pedigree | Read pedigree structure from a Plink file |
| RVPedigree | RVPedigree main function |
| RVPedigree-package | RVPedigree: A package for region-based genetic association... |
| VCC1.region | Run the VC-C1 method on a genomic region defined by a start... |
| VCC2.region | Run the VC-C2 method on a genomic region defined by a start... |
| VCC3.region | Run the VC-C3 method on a genomic region defined by a start... |
