Man pages for luannnguyen/hmfGeneAnnotation
Determines gene amplifications and biallelic losses from HMF pipeline output

annotateVariantTypeAnnotate variant type with snpEff
calcChromArmPloidiesCalculate overall chrom arm copy numbers
calcHitScoresSums the pathogenicity score of allele 1 and 2 (hit score)
detBiallHitTypeDetermine biallelic hit type
detBiallStatusDetermine biallelic hit type v2
detGeneStatusesDetermine gene amplifications and biallelic losses
detReadingFrameDetermines the reading frame in case of one or more...
ensgToHgncSymbolRetrieve HGNC symbols from a vector of ENSEMBL gene ids
extractVcfFieldsExtracts revelant fields for downstream functions and outputs...
filterVcfFilter vcf for compatibility with downstream functions
geneNamesToEnsgRetrieve ENSEMBL gene ids from a vector of gene names
getClinSigGet clinical significance by querying a tabix indexed bed...
getGeneDiplotypeMaxEffDetermine the most pathogenic diplotype effect per gene
helloHello, World!
insColAfterInsert column(s) after a column of an existing dataframe
mkClinvarTxtDownload ClinVar vcf and convert to txt file
mkGeneDiplotypesCnvMutMerge cnv and germ/som mut profiles into a table the...
mkGeneDiplotypesMutMutMerge germ/som mut profiles into a table the describes the...
mkMutProfileGeneCnvAdd annotations to the gene cnv table
mkMutProfileSnvIndelCreate annotations to the germline/somatic tables originating...
preProcessGeneCnvSubsets PURPLE gene cnv file for genes of interest
retrieveHgncGeneListRetrieve gene identifiers from HGNC
write.tsvMiscellaneous functions Write tsv file
luannnguyen/hmfGeneAnnotation documentation built on March 31, 2020, 11:03 p.m.