Man pages for Yi-Jiang/MethyGenotyper
MethylGenotyper: Accurate estimation of SNP genotypes from DNA methylation data
| backgroundCorrectionNoobFit | Fit Normal and exponential distributions (adapted from... |
| callGeno_snp | Call genotypes for SNP probes |
| callGeno_typeI | Call genotypes for Type I probes |
| callGeno_typeII | Call genotypes for Type II probes |
| call_genotypes | Call genotypes based on EM algorithm |
| constrain_R2 | Constrain R2 |
| correct_noob_dye | Noob and dye-bias correction |
| dosage2hard | Get hard genotypes from genotype probabilities |
| eBeta | Moments estimator for beta distribution (adapted from... |
| filter_by_AF | Filter by AF |
| filter_by_HWE | Filter by Hardy–Weinberg Equilibrium (HWE) p value |
| filter_by_missing | Filter by missing rate |
| filter_by_R2 | Filter by R2 |
| fit_beta_em | Estimate mixed beta distribution parameters based on EM... |
| format_genotypes | Format genotype calls |
| get_AF | Extract AFs from matching population in the 1000 Genomes... |
| get_GP_bayesian | Infer posterior genotype probabilities based on the Bayesian... |
| getHWE | Calculate Hardy-Weinberg Equilibrium (HWE) p value |
| get_indAF | Calculate individual-specific AFs |
| getKinship | Get kinship coefficients and inbreeding coefficients using... |
| getKinship_het | Get kinship coefficients using the SEEKIN-het estimator |
| getMod | Estimate mode location for each probe |
| getRAI_snp | Get RAI (Ratio of Alternative allele Intensity) for SNP... |
| getRelation | Get sample relationships |
| get_target | Get example IDAT file list |
| mnfst | EPIC manifest file |
| mnfst_450K | 450K manifest file |
| mval2beta | Convert M values to beta values |
| normExpSignal | Normal-exponential deconvolution (adapted from 'SeSAMe') |
| plot_AF | Plot the distribution of AFs in 1KGP and input data. |
| plot_PCA | To plot the projection of study samples in reference ancestry... |
| plot_RAI_distribution | Plot beta distributions for reference homozygous,... |
| pprocrustes | Projection Procrustes Analysis |
| probeInfo_snp | SNP probe information for EPIC |
| probeInfo_snp_450K | SNP probe information for 450K |
| probeInfo_typeI | Type I probe information for EPIC |
| probeInfo_typeI_450K | Type I probe information for 450K |
| probeInfo_typeII | Type II probe information for EPIC |
| probeInfo_typeII_450K | Type II probe information for 450K |
| probelist | Probe list for EPIC |
| probelist_450K | Probe list for 450K |
| procrustes | Standard Procrustes Analysis |
| projection | PCA and Procrustes analysis |
| recal_Geno | Recalibrate genotypes for samples of mixed population |
| refGeno_1KGP3 | Reference genotypes in the 1000 Genomes Project |
| refGeno_1KGP3_SNP_failQC | SNPs in 1KGP with HWE<1e-20 or F_MISSING>=0.05 |
| sam2pop | Population information for the 1KGP samples |
| TRACE | TRACE: fasT and Robust Ancestry Coordinate Estimation |
