Man pages for stefanedwards/Siccuracy
Pipeline Package for AlphaImpute
| auxfunc | Auxiliary functions |
| cbind_snp_files | Column bind files with genotype matrices |
| convert_phases | Convert phase files to genotype files. |
| convert_plink | Converts PLINK binary format to SNP formatted file. |
| convert_plinkA | Convert PLINK recoded A to SNP file. |
| deprecated | Deprecated functions |
| extract.gt | Extract genotypes from SNP objects. |
| extract.snps | #' Extracts #' #' @inheritParams extract.snps #' @return... |
| haps-format | SHAPEIT haps/sample format |
| heterozygosity | Calculates hetereozygosity stats for a single population |
| imputation_accuracy | Imputation accuracy, aka. correlations |
| mask_snp_file | Masks entries of a single SNP chip file. |
| oxford | Oxford format |
| parseformat | Format descriptors |
| rbind_snp_files | Combines rows of two SNP chip files and provides masking. |
| read.snps | Read genotype matrix from file. |
| Siccuracy | Stefan's imputation accuracy package |
| VCF-format | VCF objects in Siccuracy |
| write.snps | Write genotype matrices to file, AlphaImpute style. |
