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

Documentation for package ‘ICAMS’ version 3.0.11

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