ICAMS v2.0.7

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

Analysis and visualization of experimentally elucidated mutational signatures -- the kind of analysis and visualization in Boot et al., "In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors", Genome Research 2018, <doi:10.1101/gr.230219.117>. 'ICAMS' stands for In-depth Characterization and Analysis of Mutational Signatures. 'ICAMS' has functions to read in variant call files (VCFs) and to collate the corresponding catalogs of mutational spectra and to analyze and plot catalogs of mutational spectra and signatures. Handles both "counts-based" and "density-based" catalogs of mutational spectra or signatures.

Readme

ICAMS

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

Purpose

Analysis and visualization of experimentally elucidated mutational signatures -- the kind of analysis and visualization in Boot et al., "In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors", Genome Research 2018, https://doi.org/10.1101/gr.230219.117. 'ICAMS' stands for In-depth Characterization and Analysis of Mutational Signatures. 'ICAMS' has functions to read in variant call files (VCFs) and to collate the corresponding catalogs of mutational spectra and to analyze and plot catalogs of mutational spectra and signatures. Handles both "counts-based" and "density-based" catalogs of mutational spectra or signatures.

Installation

Install development version of ICAMS from GitHub with the R command line:

devtools::install_github("steverozen/ICAMS", ref = "v2.0.7-branch")

Reference manual

https://github.com/steverozen/ICAMS/blob/v2.0.7-branch/data-raw/ICAMS_2.0.7.pdf

Functions in ICAMS

Name Description
Canonicalize1DEL Given a deletion and its sequence context, categorize it.
CollapseCatalog "Collapse" a catalog.
AddTranscript Add transcript information to a data frame with mutation records
CheckSeqContextInVCF Check that the sequence context information is consistent with the value of the column REF.
Canonicalize1INS Given an insertion and its sequence context, categorize it.
CatalogRowOrder Standard order of row names in a catalog.
AddAndCheckSequenceID Add sequence context to a data frame with ID (insertion/deletion) mutation records, and confirm that they match the given reference genome.
CanonicalizeID Given vectors of insertions and deletions in contexts categorize them.
Canonicalize1ID Given a single insertion or deletion in context categorize it.
CreateOneColDBSMatrix Create double base catalog for *one* sample from a Variant Call Format (VCF) file
CreateOneColSBSMatrix Create the matrix an SBS catalog for *one* sample from an in-memory VCF.
GetStrandedKmerCounts Generate stranded k-mer abundance from a given genome and gene annotation file
PlotPPM Plot position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.
CreateExomeStrandedRanges Create exome transcriptionally stranded regions
GetGenomeKmerCounts Generate k-mer abundance from a given genome
PlotCatalogToPdf Plot catalog to a PDF file.
CreateDinucAbundance Create dinucleotide abundance
GetSequenceKmerCounts Generate k-mer abundance from given nucleotide sequences
GetExomeKmerCounts Generate exome k-mer abundance from a given reference genome
ReadCatalog Read catalog.
AddSeqContext Add sequence context to a data frame with mutation records
CreateOnePPMFromSBSVCF Create position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.
CreateTrinucAbundance Create trinucleotide abundance
InferAbundance Infer abundance given a matrix-like object and additional information.
FindDelMH Return the length of microhomology at a deletion.
ReadMutectVCF Read in the data lines of a Variant Call Format (VCF) file created by MuTect
ReadStrelkaSBSVCFs Read Strelka SBS (single base substitutions) VCF files.
CreateOneColIDMatrix Create one column of the matrix for an indel catalog from *one* in-memory VCF.
ReadMutectVCFs Read Mutect VCF files.
ReadTranscriptRanges Read transcript ranges and strand information from a gff3 format file. Use this one for the new, cut down gff3 file (2018 11 24)
InferClassOfCatalogForRead Infer the class of catalog in a file.
CreatePPMFromSBSVCFs Create position probability matrices (PPM) from a list of SBS vcfs
CreateTetranucAbundance Create tetranucleotide abundance
ReadAndSplitMutectVCFs Read and split Mutect VCF files.
ReadBedRanges Read chromosome and position information from a bed format file.
ReadAndSplitStrelkaSBSVCFs Read and split Strelka SBS VCF files.
PlotPPMToPdf Plot position probability matrices (PPM) to a PDF file
WriteCat Write a catalog to a file.
all.abundance K-mer abundances.
TCFromCouSigCou Source catalog type is counts or counts.signature
WriteCatalog Write a catalog
TCFromDenSigDen density -> <anything> density.signature -> density.signature, counts.signature
CreateTransRanges Create a transcript range file from the raw GFF3 File
SplitStrelkaSBSVCF Split an in-memory Strelka VCF into SBS, DBS, and variants involving > 2 consecutive bases
GetVAF Extract the VAFs (variant allele frequencies) from a VCF file.
StandardChromName Standardize the chromosome name annotations for a data frame.
revc Reverse complement every string in string.vec.
TestMakeCatalogFromStrelkaSBSVCFs This function is to make catalogs from the sample Strelka SBS VCF files to compare with the expected catalog information.
StopIfRegionIllegal Stop if region is illegal.
ReadDukeNUSCat192 Read a 192-channel spectra (or signature) catalog in Duke-NUS format.
StopIfTranscribedRegionIllegal Stop if region is illegal for an in-transcript catalogs
TranscriptRanges Transcript ranges data
StopIfCatalogTypeIllegal Stop if catalog.type is illegal.
StopIfNrowIllegal Stop if the number of rows in object is illegal
TestMakeCatalogFromMutectVCFs This function makes catalogs from the sample Mutect VCF file and compares it with the expected catalog information.
CreateStrandedDinucAbundance Create stranded dinucleotide abundance
CreateStrandedTrinucAbundance Create stranded trinucleotide abundance
FindMaxRepeatDel Return the number of repeat units in which a deletion is embedded.
CreatePentanucAbundance Create pentanucleotide abundance
FindMaxRepeatIns Return the number of repeat units in which an insertion is embedded.
ReadStrelkaIDVCFs Read Strelka ID (insertion and deletion) VCF files.
MutectVCFFilesToCatalog Create SBS, DBS and Indel catalogs from Mutect VCF files
ICAMS ICAMS: In-depth Characterization and Analysis of Mutational Signatures
MutectVCFFilesToCatalogAndPlotToPdf Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF
ReadStrelkaSBSVCF Read in the data lines of an SBS VCF created by Strelka version 1
GenerateEmptyKmerCounts Generate an empty matrix of k-mer abundance
RemoveRangesOnBothStrand Remove ranges that fall on both strands
TestMakeCatalogFromStrelkaIDVCFs This function is to make catalogs from the sample Strelka ID VCF files to compare with the expected catalog information.
as.catalog Create a catalog from a numeric matrix or numeric data.frame.
MakeDataFrameFromMutectVCF Read in the data lines of a Variant Call Format (VCF) file created by MuTect
IsGRCh37 Test if object is BSgenome.Hsapiens.1000genome.hs37d5.
IsGRCm38 Test if object is BSgenome.Mmusculus.UCSC.mm10.
GenerateKmer Generate all possible k-mers of length k.
IsGRCh38 Test if object is BSgenome.Hsapiens.UCSC.hg38.
NormalizeGenomeArg Take strings representing a genome and return the BSgenome object.
MakeDataFrameFromStrelkaSBSVCF Read in the data lines of an SBS VCF created by Strelka version 1
RevcDBS144 Reverse complement strings that represent stranded DBSs
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
RevcSBS96 Reverse complement strings that represent stranded SBSs
PlotCatalog Plot one spectrum or signature.
SplitListOfMutectVCFs Split each Mutect VCF into SBS, DBS, and ID VCFs (plus two VCF-like data frame with left-over rows).
SplitListOfStrelkaSBSVCFs Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving > 2 consecutive bases
MakeVCFDBSdf MakeVCFDBSdf Take DBS ranges and the original VCF and generate a VCF with dinucleotide REF and ALT alleles.
ReadStapleGT96SBS Read a 96-channel spectra (or signature) catalog where rownames are e.g. "A[C>A]T"
ReadStrelkaIDVCF Read in the data lines of an ID VCF created by Strelka version 1
SplitOneMutectVCF Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
StrelkaIDVCFFilesToCatalogAndPlotToPdf Create ID (indel) catalog from Strelka ID VCF files and plot them to PDF
StrelkaIDVCFFilesToCatalog Create ID (indel) catalog from Strelka ID VCF files
VCFsToIDCatalogs Create ID (insertion and deletion) catalog from ID VCFs
VCFsToSBSCatalogs Create SBS catalogs from SBS VCFs
TransformCatalog Transform between counts and density spectrum catalogs and counts and density signature catalogs.
VCFsToDBSCatalogs Create DBS catalogs from VCFs
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Details

Type Package
License GPL-3
URL https://github.com/steverozen/ICAMS
BugReports https://github.com/steverozen/ICAMS/issues
Encoding UTF-8
LazyData true
Language en-US
biocViews
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2019-07-08 03:20:22 UTC; steve
Repository CRAN
Date/Publication 2019-07-11 12:53:11 UTC

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