Man pages for danjlawson/pcapred
Produce PC Eigenvector Predictions From Plink Input Data And Loadings
| bedasbigmatrix | Get Bed Data As A BigMatrix |
| bedashap | Convert Rbed object to binary haplotype format |
| bedasmatrix | Get Bed Data As A Matrix |
| get_data | Get normalised data from an rbed object in an efficient... |
| getfreqs | Compute the allele frequencies for bed file |
| getind | Extract a individual from a binary format bed object |
| getinds | Extract a chunk of individuals from a binary format bed... |
| getsnp | Extract a SNP from a binary format bed object |
| mergeref | Merge your dataset into a reference using the efficient... |
| normalise | Normalise SNPs according to a reference frequency under a... |
| normalisesnp | Normalise SNPs according to a reference frequency under a... |
| pcapred-package | pcapred: Produce PC Eigenvector Predictions From Plink Input... |
| pred_flash_missing | Create predictions for eigenvalues from flashpca-scaled data |
| pred_flash_simple | Create predictions for eigenvalues from flashpca-scaled data |
| predictpcs | Create predictions for eigenvalues from binary stored data |
| pred_missing | Create predictions for eigenvalues when there is missing data |
| pred_plink_missing | Create predictions for eigenvalues from flashpca-scaled data |
| pred_plink_simple | Create predictions for eigenvalues from plink-scaled data |
| pred_simple | Create predictions for eigenvalues when there is no missing... |
| readbed | Read the binary PLINK format (BED, BIM, and FAM) efficiently |
| readinput | Read the target dataset |
| readpcs | Read the target dataset |
| readreference | Read the Reference Data for a PC projection |
| readsnpstats | Read the snp stats |
| readsnpweights | Read Snp Weights/Loadings from a file |
| test_pca | Test PCA predictions with access to the truth |
| transform_flashref | Create direct SNP weights from a flashpca-like (scaled)... |
| transform_pcs | Create direct SNP weights from a reference |
| transform_plinkref | Create direct SNP weights from a plink-like (scaled)... |
| writebinhap | Convert binary haplotype format to hex formatted output file |
| writepred | Write Predicted PCs In Standard Format |
