# In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

## Documentation for package ‘ICAMS’ version 3.0.11

- DESCRIPTION file.
- Package NEWS.

## Help Pages

all.abundance | K-mer abundances
AnnotateDBSVCF | Add sequence context and transcript information to an in-memory DBS VCF
AnnotateIDVCF | Add sequence context and transcript information to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome
AnnotateSBSVCF | Add sequence context and transcript information to an in-memory SBS VCF
as.catalog | Create a catalog from a 'matrix', 'data.frame', or 'vector'
Canonicalize1Del | Given a deletion and its sequence context, categorize it
catalog.row.order | Standard order of row names in a catalog
CatalogRowOrder | Standard order of row names in a catalog
Collapse144CatalogTo78 | "Collapse" a catalog
Collapse1536CatalogTo96 | "Collapse" a catalog
Collapse192CatalogTo96 | "Collapse" a catalog
CollapseCatalog | "Collapse" a catalog
ConvertCatalogToSigProfilerFormat | Covert an ICAMS Catalog to SigProfiler format
FindDelMH | Return the length of microhomology at a deletion
FindMaxRepeatDel | Return the number of repeat units in which a deletion is embedded
gene.expression.data.HepG2 | Example gene expression data from two cell lines
gene.expression.data.MCF10A | Example gene expression data from two cell lines
GeneExpressionData | Example gene expression data from two cell lines
GetFreebayesVAF | Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
GetMutectVAF | Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
GetPCAWGConsensusVAF | Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
GetStrelkaVAF | Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
GetVAF | Extract the VAFs (variant allele frequencies) and read depth information from a VCF file
ICAMS | ICAMS: In-depth Characterization and Analysis of Mutational Signatures
IsICAMSCatalog | Check whether an R object contains one of the ICAMS catalog classes
MutectVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "mutect") instead]* Create SBS, DBS and Indel catalogs from Mutect VCF files
MutectVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "mutect") instead]* Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF
MutectVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "mutect") instead]* Create a zip file which contains catalogs and plot PDFs from Mutect VCF files
PlotCatalog | Plot *one* spectrum or signature
PlotCatalogToPdf | Plot catalog to a PDF file
PlotTransBiasGeneExp | Plot transcription strand bias with respect to gene expression values
PlotTransBiasGeneExpToPdf | Plot transcription strand bias with respect to gene expression values to a PDF file
ReadAndSplitMutectVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller = "mutect") instead]* Read and split Mutect VCF files
ReadAndSplitStrelkaSBSVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]* Read and split Strelka SBS VCF files
ReadAndSplitVCFs | Read and split VCF files
ReadCatalog | Read catalog
ReadStrelkaIDVCFs | *[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]* Read Strelka ID (small insertions and deletions) VCF files
ReadVCFs | Read VCF files
revc | Reverse complement every string in 'string.vec'
SimpleReadVCF | Read a VCF file into a data frame with minimal processing.
SplitListOfVCFs | Split each VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame with left-over rows)
StrelkaIDVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]* Create ID (small insertions and deletions) catalog from Strelka ID VCF files
StrelkaIDVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka") instead]* Create ID (small insertions and deletions) catalog from Strelka ID VCF files and plot them to PDF
StrelkaIDVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]* Create a zip file which contains ID (small insertions and deletions) catalog and plot PDF from Strelka ID VCF files
StrelkaSBSVCFFilesToCatalog | *[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]* Create SBS and DBS catalogs from Strelka SBS VCF files
StrelkaSBSVCFFilesToCatalogAndPlotToPdf | *[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka") instead]* Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF
StrelkaSBSVCFFilesToZipFile | *[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]* Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF files
trans.ranges.GRCh37 | Transcript ranges data
trans.ranges.GRCh38 | Transcript ranges data
trans.ranges.GRCm38 | Transcript ranges data
TranscriptRanges | Transcript ranges data
TransformCatalog | Transform between counts and density spectrum catalogs and counts and density signature catalogs
VCFsToCatalogs | Create SBS, DBS and Indel catalogs from VCFs
VCFsToCatalogsAndPlotToPdf | Create SBS, DBS and Indel catalogs from VCFs and plot them to PDF
VCFsToDBSCatalogs | Create DBS catalogs from VCFs
VCFsToIDCatalogs | Create ID (small insertions and deletions) catalog from ID VCFs
VCFsToSBSCatalogs | Create SBS catalogs from SBS VCFs
VCFsToZipFile | Create a zip file which contains catalogs and plot PDFs from VCFs
WriteCatalog | Write a catalog