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

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Documentation for package ‘ICAMS’ version 2.3.12

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all.abundance K-mer abundances
AnnotateDBSVCF Add sequence context and transcript information to an in-memory DBS VCF
AnnotateIDVCF Add sequence context 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
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
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
MutectVCFFilesToCatalog Create SBS, DBS and Indel catalogs from Mutect VCF files
MutectVCFFilesToCatalogAndPlotToPdf Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF
MutectVCFFilesToZipFile 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 Read and split Mutect VCF files
ReadAndSplitStrelkaSBSVCFs Read and split Strelka SBS VCF files
ReadAndSplitVCFs Read and split VCF files
ReadCatalog Read catalog
ReadStrelkaIDVCFs Read Strelka ID (small insertion and deletion) VCF files
revc Reverse complement every string in 'string.vec'
StrelkaIDVCFFilesToCatalog Create ID (small insertion and deletion) catalog from Strelka ID VCF files
StrelkaIDVCFFilesToCatalogAndPlotToPdf Create ID (small insertion and deletion) catalog from Strelka ID VCF files and plot them to PDF
StrelkaIDVCFFilesToZipFile Create a zip file which contains ID (small insertion and deletion) catalog and plot PDF from Strelka ID VCF files
StrelkaSBSVCFFilesToCatalog Create SBS and DBS catalogs from Strelka SBS VCF files
StrelkaSBSVCFFilesToCatalogAndPlotToPdf Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF
StrelkaSBSVCFFilesToZipFile 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 insertion and deletion) 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