Man pages for luannnguyen/hmfGeneAnnotation
Determines gene amplifications and biallelic losses from HMF pipeline output
| annotateVariantType | Annotate variant type with snpEff |
| calcChromArmPloidies | Calculate overall chrom arm copy numbers |
| calcHitScores | Sums the pathogenicity score of allele 1 and 2 (hit score) |
| detBiallHitType | Determine biallelic hit type |
| detBiallStatus | Determine biallelic hit type v2 |
| detGeneStatuses | Determine gene amplifications and biallelic losses |
| detReadingFrame | Determines the reading frame in case of one or more... |
| ensgToHgncSymbol | Retrieve HGNC symbols from a vector of ENSEMBL gene ids |
| extractVcfFields | Extracts revelant fields for downstream functions and outputs... |
| filterVcf | Filter vcf for compatibility with downstream functions |
| geneNamesToEnsg | Retrieve ENSEMBL gene ids from a vector of gene names |
| getClinSig | Get clinical significance by querying a tabix indexed bed... |
| getGeneDiplotypeMaxEff | Determine the most pathogenic diplotype effect per gene |
| hello | Hello, World! |
| insColAfter | Insert column(s) after a column of an existing dataframe |
| mkClinvarTxt | Download ClinVar vcf and convert to txt file |
| mkGeneDiplotypesCnvMut | Merge cnv and germ/som mut profiles into a table the... |
| mkGeneDiplotypesMutMut | Merge germ/som mut profiles into a table the describes the... |
| mkMutProfileGeneCnv | Add annotations to the gene cnv table |
| mkMutProfileSnvIndel | Create annotations to the germline/somatic tables originating... |
| preProcessGeneCnv | Subsets PURPLE gene cnv file for genes of interest |
| retrieveHgncGeneList | Retrieve gene identifiers from HGNC |
| write.tsv | Miscellaneous functions Write tsv file |
