Man pages for NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq
HLA typing clustering and visualization based on specific similarity metrics
| calculateHamming | Calculate Hamming distance between all samples |
| demoHLADataset | The HLA typing information from multiple samples stored in a... |
| draw_dendrogram | Draw dendrogram |
| draw_heatmap | Draw sample-to-sample heatmap |
| example_sample_pair_data | This dataset contains the allele information for HLA genes in... |
| extractRef | Process the line contening the reference sequence |
| extractSeq | Process the line containing the alignment to the reference |
| extractTyping | Extract the HLA typing string from one line of aligment |
| getIncompleteTypingPos | Get the position in the HLA table of the corresponding HLA... |
| getSeqCMP | Get the subsequences from 2 allele types from the same HLA... |
| getSubSeq | Get the subsequence |
| getTypingPos | Get the position in the HLA table of the corresponding HLA... |
| hamming_distance_digit1 | Compute the Hamming distance between two samples |
| hclustHLA | Hierarchical clustering using a HLA typing similarity metric |
| HLAClustRView-package | HLAClustRView: HLA typing clustering and visualization based... |
| HLADataset | Print a 'HLADataset' object |
| hladb_protein_3.35.0 | This dataset contains the protein information from the HLA... |
| HLAMetric | Print a 'HLAMetric' object |
| loadHLADb | load HLA Database alignment files for a specific alignment... |
| makeDistanceMatrix | Convert distance table to distance matrix |
| parseAlignment | Pre-process HLA Database alignment file |
| parse_hla_dataset | Convert data.frame with HLA typing information to tibble... |
| parseHLADbAlignment | Parse HLA Database alignment files for a specific alignment... |
| parseSubMatrix | load matrix of substitution |
| readHLADataset | Extract HLA typing information for all samples present in a... |
| reduceTypingPos | Verify if all the sequence are the same for the typing... |
| sample_pair_distance | Sample Pair Distance |
| splitTyping | Split a HLA allele name into a matrix of fields |
