| AddAndCheckDBSClassInVCF | Add and check DBS class in an annotated VCF with the... |
| AddAndCheckSBSClassInVCF | Add and check SBS class in an annotated VCF with the... |
| AddDBSClass | Add DBS mutation class to an annotated DBS VCF |
| AddRunInformation | Create a run information text file from generating zip... |
| AddSBSClass | Add SBS mutation class to an annotated SBS VCF |
| AddSeqContext | Add sequence context to a data frame with mutation records |
| AddTranscript | Add transcript information to a data frame with mutation... |
| all.abundance | K-mer abundances |
| AnnotateDBSVCF | Add sequence context and transcript information to an... |
| AnnotateIDVCF | Add sequence context and transcript information to an... |
| AnnotateSBSVCF | Add sequence context and transcript information to an... |
| as.catalog | Create a catalog from a 'matrix', 'data.frame', or 'vector' |
| CalBaseCountsFrom3MerAbundance | Calculate base counts from three mer abundance |
| CalculateNumberOfSpace | Calculate the number of space needed to add strand bias... |
| Canonicalize1Del | Given a deletion and its sequence context, categorize it |
| Canonicalize1ID | Given a single insertion or deletion in context categorize... |
| Canonicalize1INS | Given an insertion and its sequence context, categorize it. |
| CanonicalizeID | Determine the mutation types of insertions and deletions. |
| CatalogRowOrder | Standard order of row names in a catalog |
| CheckAndFixChrNames | Check and, if possible, correct the chromosome names in a VCF... |
| CheckAndFixChrNamesForTransRanges | Check and, if possible, correct the chromosome names in a... |
| CheckAndReorderRownames | Check whether the rownames of 'object' are correct, if yes... |
| CheckAndReturnDBSCatalogs | Check and return DBS catalogs |
| CheckAndReturnDBSMatrix | Check and return the DBS mutation matrix |
| CheckAndReturnIDCatalog | Check and return ID catalog |
| CheckAndReturnIDMatrix | Check and return the ID mutation matrix |
| CheckAndReturnSBSCatalogs | Check and return SBS catalogs |
| CheckAndReturnSBSMatrix | Check and return the SBS mutation matrix |
| CheckDBSClassInVCF | Check DBS mutation class in VCF with the corresponding DBS... |
| CheckSBSClassInVCF | Check SBS mutation class in VCF with the corresponding SBS... |
| CheckSeqContextInVCF | Check that the sequence context information is consistent... |
| CollapseCatalog | "Collapse" a catalog |
| ConvertCatalogToSigProfilerFormat | Covert an ICAMS Catalog to SigProfiler format |
| ConvertICAMSCatalogToSigProSBS96 | Covert an ICAMS SBS96 Catalog to SigProfiler format |
| CreateDinucAbundance | Create dinucleotide abundance |
| CreateExomeStrandedRanges | Create exome transcriptionally stranded regions |
| CreateOneColDBSMatrix | Create the matrix a DBS catalog for *one* sample from an... |
| CreateOneColIDMatrix | Create one column of the matrix for an indel catalog from... |
| CreateOneColSBSMatrix | Create the matrix an SBS catalog for *one* sample from an... |
| CreateOnePPMFromSBSVCF | Create position probability matrix (PPM) for *one* sample... |
| CreatePentanucAbundance | Create pentanucleotide abundance |
| CreatePPMFromSBSVCFs | Create position probability matrices (PPM) from a list of SBS... |
| CreateStrandedDinucAbundance | Create stranded dinucleotide abundance |
| CreateStrandedTrinucAbundance | Create stranded trinucleotide abundance |
| CreateTetranucAbundance | Create tetranucleotide abundance |
| CreateTransRanges | Create a transcript range file from the raw GFF3 File |
| CreateTrinucAbundance | Create trinucleotide abundance |
| FindDelMH | Return the length of microhomology at a deletion |
| FindMaxRepeatDel | Return the number of repeat units in which a deletion is... |
| FindMaxRepeatIns | Return the number of repeat units in which an insertion is... |
| GeneExpressionData | Example gene expression data from two cell lines |
| GenerateEmptyKmerCounts | Generate an empty matrix of k-mer abundance |
| GenerateKmer | Generate all possible k-mers of length k. |
| GeneratePlotPFMmatrix | Generate PFMmatrix (Position Frequency Matrix) from a given... |
| GenerateVCFsFromIndelSimpleFile1 | Generate reconstructed VCFs from indel (small insertions and... |
| GenerateVCFsFromIndelSimpleFiles | Generate reconstructed VCFs from indel (small insertions and... |
| Get1BPIndelFlanks | Get all the sequence contexts of the indels in a given 1... |
| GetCustomKmerCounts | Generate custom k-mer abundance from a given reference genome |
| GetGenomeKmerCounts | Generate k-mer abundance from a given genome |
| GetMutationLoadsFromMutectVCFs | Get mutation loads information from Mutect VCF files. |
| GetMutationLoadsFromStrelkaIDVCFs | Get mutation loads information from Strelka ID VCF files. |
| GetMutationLoadsFromStrelkaSBSVCFs | Get mutation loads information from Strelka SBS VCF files. |
| GetSequenceKmerCounts | Generate k-mer abundance from given nucleotide sequences |
| GetStrandedKmerCounts | Generate stranded k-mer abundance from a given genome and... |
| GetVAF | Extract the VAFs (variant allele frequencies) and read depth... |
| HaplotypePlot | Generate Haplotype plot from a given list of sequences |
| ICAMS | ICAMS: In-depth Characterization and Analysis of Mutational... |
| InferAbundance | Infer 'abundance' given a matrix-like 'object' and additional... |
| InferCatalogClassPrefix | These two functions is applicable only for internal... |
| InferCatalogInfo | This function converts an data.table imported from external... |
| InferRefGenomeName | Infer reference genome name from a character string |
| InferRownames | Infer the correct rownames for a matrix based on its number... |
| IsGRCh37 | Test if object is 'BSgenome.Hsapiens.1000genome.hs37d5'. |
| IsGRCh38 | Test if object is 'BSgenome.Hsapiens.UCSC.hg38'. |
| IsGRCm38 | Test if object is 'BSgenome.Mmusculus.UCSC.mm10'. |
| IsICAMSCatalog | Check whether an R object contains one of the ICAMS catalog... |
| IsRefGenomeInstalled | Check whether the BSgenome package is installed |
| MakeDataFrameFromVCF | Read in the data lines of a Variant Call Format (VCF) file |
| MakeVCFDBSdf | MakeVCFDBSdf Take DBS ranges and the original VCF and... |
| MutectVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "mutect")... |
| MutectVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller =... |
| MutectVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "mutect")... |
| NormalizeGenomeArg | Take strings representing a genome and return the 'BSgenome'... |
| Plot96PartOfCompositeToPDF | Plot the SBS96 part of a SignatureAnalyzer COMPOSITE... |
| PlotCatalog | Plot *one* spectrum or signature |
| PlotCatalogToPdf | Plot catalog to a PDF file |
| PlotPFMmatrix | Generate dot-line plot for sequence contest of 1bp indel |
| PlotPPM | Plot position probability matrix (PPM) for *one* sample from... |
| PlotPPMToPdf | Plot position probability matrices (PPM) to a PDF file |
| PlotTransBiasGeneExp | Plot transcription strand bias with respect to gene... |
| PlotTransBiasGeneExpToPdf | Plot transcription strand bias with respect to gene... |
| ReadAndSplitMutectVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller = "mutect")... |
| ReadAndSplitStrelkaSBSVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller =... |
| ReadAndSplitVCFs | Read and split VCF files |
| ReadBedRanges | Read chromosome and position information from a bed format... |
| ReadCatalog | Read catalog |
| ReadCatalogErrReturn | Get error message and either stop or create a null error... |
| ReadCatalogInternal | Internal read catalog function to be wrapped in a tryCatch |
| ReadDukeNUSCat192 | Read a 192-channel spectra (or signature) catalog in Duke-NUS... |
| ReadMutectVCF | Read in the data lines of a Variant Call Format (VCF) file... |
| ReadMutectVCFs | Read Mutect VCF files. |
| ReadStapleGT96SBS | Read a 96-channel spectra (or signature) catalog where... |
| ReadStrelkaIDVCF | Read in the data lines of an ID VCF created by Strelka... |
| ReadStrelkaIDVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller =... |
| ReadStrelkaSBSVCF | Read in the data lines of an SBS VCF created by Strelka... |
| ReadStrelkaSBSVCFs | Read Strelka SBS (single base substitutions) VCF files. |
| ReadTranscriptRanges | Read transcript ranges and strand information from a gff3... |
| ReadVCF | Read in the data lines of a Variant Call Format (VCF) file |
| ReadVCFs | Read VCF files |
| RemoveRangesOnBothStrand | Remove ranges that fall on both strands |
| RenameColumnsWithNameEnd | Is there any column in 'df' with name "end"? If there is,... |
| RenameColumnsWithNameStart | Is there any column in 'df' with name "start"? If there is,... |
| RenameColumnsWithNameStrand | Is there any column in 'df' with name "strand"? If there is,... |
| RenameColumnsWithNameVAF | Is there any column in 'df' with name "VAF"? If there is,... |
| Restaple1536 | Convert 1536-channel mutation-type identifiers like this... |
| Restaple96 | Convert 96-channel mutation-type identifiers like this... |
| revc | Reverse complement every string in 'string.vec' |
| RevcDBS144 | Reverse complement strings that represent stranded DBSs |
| RevcSBS96 | Reverse complement strings that represent stranded SBSs |
| SelectVariantsByChromName | Select variants according to chromosome names specified by... |
| SimpleReadVCF | Read a VCF file into a data frame with minimal processing. |
| SplitListOfMutectVCFs | Split each Mutect VCF into SBS, DBS, and ID VCFs (plus... |
| SplitListOfStrelkaSBSVCFs | Split a list of in-memory Strelka SBS VCF into SBS, DBS, and... |
| SplitListOfVCFs | Split each VCF into SBS, DBS, and ID VCFs (plus VCF-like data... |
| SplitOneMutectVCF | Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list... |
| SplitOneVCF | Split a VCF into SBS, DBS, and ID VCFs, plus a list of other... |
| SplitSBSVCF | Split an in-memory SBS VCF into pure SBSs, pure DBSs, and... |
| SplitStrelkaSBSVCF | Split an in-memory Strelka VCF into SBS, DBS, and variants... |
| StandardChromName | Standardize the chromosome name annotations for a data frame. |
| StandardChromNameNew | Standardize the chromosome name annotations for a data frame. |
| StopIfCatalogTypeIllegal | Stop if 'catalog.type' is illegal. |
| StopIfNrowIllegal | Stop if the number of rows in 'object' is illegal |
| StopIfRegionIllegal | Stop if 'region' is illegal. |
| StopIfTranscribedRegionIllegal | Stop if 'region' is illegal for an in-transcript catalogs |
| StrelkaIDVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "strelka")... |
| StrelkaIDVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller =... |
| StrelkaIDVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "strelka")... |
| StrelkaSBSVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "strelka")... |
| StrelkaSBSVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller =... |
| StrelkaSBSVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "strelka")... |
| SymmetricalContextsFor1BPIndel | Get all the sequence contexts of the indels in a given 1... |
| TCFromCouSigCou | Source catalog type is counts or counts.signature |
| TCFromDenSigDen | density -> <anything> density.signature -> density.signature,... |
| TestMakeCatalogFromMutectVCFs | This function makes catalogs from the sample Mutect VCF file... |
| TestMakeCatalogFromStrelkaIDVCFs | This function is to make catalogs from the sample Strelka ID... |
| TestMakeCatalogFromStrelkaSBSVCFs | This function is to make catalogs from the sample Strelka SBS... |
| TestPlotCatCOMPOSITE | Plot the a SignatureAnalyzer COMPOSITE signature or catalog... |
| TranscriptRanges | Transcript ranges data |
| TransformCatalog | Transform between counts and density spectrum catalogs and... |
| TransRownames.ID.PCAWG.SigPro | For indels, convert ICAMS/PCAWG7 rownames into SigProfiler... |
| TransRownames.ID.SigPro.PCAWG | For indels, convert SigProfiler rownames into ICAMS/PCAWG7... |
| Unstaple1536 | Convert SBS1536-channel mutations-type identifiers like this... |
| Unstaple78 | Convert DBS78-channel mutations-type identifiers like this... |
| Unstaple96 | Convert SBS96-channel mutations-type identifiers like this... |
| VCFsToCatalogs | Create SBS, DBS and Indel catalogs from VCFs |
| VCFsToCatalogsAndPlotToPdf | Create SBS, DBS and Indel catalogs from VCFs and plot them to... |
| VCFsToDBSCatalogs | Create DBS catalogs from VCFs |
| VCFsToIDCatalogs | Create ID (small insertions and deletions) catalog from ID... |
| VCFsToSBSCatalogs | Create SBS catalogs from SBS VCFs |
| VCFsToZipFile | Create a zip file which contains catalogs and plot PDFs from... |
| VCFsToZipFileXtra | Analogous to 'VCFsToZipFile', also generates density CSV and... |
| WriteCat | Write a catalog to a file. |
| WriteCatalog | Write a catalog |
| WriteCatalogIndelSigPro | Write Indel Catalogs in SigProExtractor format |
