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ICAMS

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 the stable version of ICAMS from CRAN with the R command line:

install.packages("ICAMS")

After that, install the necessary dependency package from Bioconductor in order to successfully load ICAMS:

install.packages("BiocManager")
BiocManager::install("BSgenome")

Development version

To use new features, you can install ICAMS from the master branch on GitHub, which may not be stable:

install.packages("devtools")
devtools::install_github("steverozen/ICAMS")

Reference manual

https://github.com/steverozen/ICAMS/blob/master/data-raw/ICAMS_2.0.10.pdf

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Version

Install

install.packages('ICAMS')

Monthly Downloads

563

Version

2.0.10

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/steverozen/ICAMS

Maintainer

Steve Rozen

Last Published

December 13th, 2019

Functions in ICAMS (2.0.10)

CreateDinucAbundance

Create dinucleotide abundance

Add transcript information to a data frame with mutation records

CreateOneColIDMatrix

Create one column of the matrix for an indel catalog from *one* in-memory VCF.

CreateOneColDBSMatrix

Create the matrix a DBS catalog for *one* sample from an in-memory VCF.

FindMaxRepeatDel

Return the number of repeat units in which a deletion is embedded.

GetStrandedKmerCounts

Generate stranded k-mer abundance from a given genome and gene annotation file

CheckSeqContextInVCF

Check that the sequence context information is consistent with the value of the column REF.

CreateTetranucAbundance

Create tetranucleotide abundance

CheckAndFixChrNames

Check and, if possible, correct the chromosome names in a VCF data.frame.

CreateTransRanges

Create a transcript range file from the raw GFF3 File

CheckAndReorderRownames

Check whether the rownames of object are correct, if yes then put the rows in the correct order.

CollapseCatalog

"Collapse" a catalog.

MakeDataFrameFromStrelkaSBSVCF

Read in the data lines of an SBS VCF created by Strelka version 1

Plot position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.

MakeVCFDBSdf Take DBS ranges and the original VCF and generate a VCF with dinucleotide REF and ALT alleles.

Extract the VAFs (variant allele frequencies) from a VCF file.

CreateStrandedDinucAbundance

Create stranded dinucleotide abundance

FindMaxRepeatIns

Return the number of repeat units in which an insertion is embedded.

GeneExpressionData

Example gene expression data from two cell lines.

CreateStrandedTrinucAbundance

Create stranded trinucleotide abundance

ICAMS: In-depth Characterization and Analysis of Mutational Signatures

Return the length of microhomology at a deletion.

InferClassOfCatalogForRead

Infer the class of catalog in a file.

CreateTrinucAbundance

Create trinucleotide abundance

CreateExomeStrandedRanges

Create exome transcriptionally stranded regions

GetSequenceKmerCounts

Generate k-mer abundance from given nucleotide sequences

Infer abundance given a matrix-like object and additional information.

GetGenomeKmerCounts

Generate k-mer abundance from a given genome

Infer the correct rownames for a matrix based on its number of rows

Plot one spectrum or signature.

Plot96PartOfCompositeToPDF

Plot the SBS96 part of a SignatureAnalyzer COMPOSITE signature or catalog

CreatePPMFromSBSVCFs

Create position probability matrices (PPM) from a list of SBS vcfs

MutectVCFFilesToCatalogAndPlotToPdf

Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF

CreateOnePPMFromSBSVCF

Create position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file.

CreatePentanucAbundance

Create pentanucleotide abundance

GetExomeKmerCounts

Generate exome k-mer abundance from a given reference genome

Generate all possible k-mers of length k.

CreateOneColSBSMatrix

Create the matrix an SBS catalog for *one* sample from an in-memory VCF.

MutectVCFFilesToCatalog

Create SBS, DBS and Indel catalogs from Mutect VCF files

NormalizeGenomeArg

Take strings representing a genome and return the BSgenome object.

GenerateEmptyKmerCounts

Generate an empty matrix of k-mer abundance

RemoveRangesOnBothStrand

Remove ranges that fall on both strands

VCFsToIDCatalogs

Create ID (small insertion and deletion) catalog from ID VCFs

StrelkaIDVCFFilesToCatalog

Create ID (small insertion and deletion) catalog from Strelka ID VCF files

ReadDukeNUSCat192

Read a 192-channel spectra (or signature) catalog in Duke-NUS format.

TranscriptRanges

Transcript ranges data

TransformCatalog

Transform between counts and density spectrum catalogs and counts and density signature catalogs.

StrelkaIDVCFFilesToCatalogAndPlotToPdf

Create ID (small insertion and deletion) catalog from Strelka ID VCF files and plot them to PDF

PlotCatalogToPdf

Plot catalog to a PDF file.

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)

Read in the data lines of a Variant Call Format (VCF) file created by Mutect

VCFsToSBSCatalogs

Create SBS catalogs from SBS VCFs

ReadAndSplitStrelkaSBSVCFs

Read and split Strelka SBS VCF files.

ReadStrelkaIDVCFs

Read Strelka ID (small insertion and deletion) VCF files.

SplitOneMutectVCF

Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations

MakeDataFrameFromMutectVCF

Read in the data lines of a Variant Call Format (VCF) file created by Mutect

Plot position probability matrices (PPM) to a PDF file

Test if object is BSgenome.Mmusculus.UCSC.mm10.

ReadAndSplitMutectVCFs

Read and split Mutect VCF files.

SplitListOfStrelkaSBSVCFs

Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving > 2 consecutive bases

ReadStrelkaIDVCF

Read in the data lines of an ID VCF created by Strelka version 1

ReadStrelkaSBSVCF

Read in the data lines of an SBS VCF created by Strelka version 1

Test if object is BSgenome.Hsapiens.1000genome.hs37d5.

Test if object is BSgenome.Hsapiens.UCSC.hg38.

ReadStrelkaSBSVCFs

Read Strelka SBS (single base substitutions) VCF files.

PlotTransBiasGeneExp

Plot transcription strand bias with respect to gene expression values.

ReadStapleGT96SBS

Read a 96-channel spectra (or signature) catalog where rownames are e.g. "A[C>A]T".

SplitListOfMutectVCFs

Split each Mutect VCF into SBS, DBS, and ID VCFs (plus two VCF-like data frame with left-over rows).

Read Mutect VCF files.

Reverse complement strings that represent stranded SBSs

PlotTransBiasGeneExpToPdf

Plot transcription strand bias with respect to gene expression values to a PDF file.

StrelkaSBSVCFFilesToCatalog

Create SBS and DBS catalogs from Strelka SBS VCF files.

SplitStrelkaSBSVCF

Split an in-memory Strelka VCF into SBS, DBS, and variants involving > 2 consecutive bases

StrelkaSBSVCFFilesToCatalogAndPlotToPdf

Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF

Read chromosome and position information from a bed format file.

RenameColumnsWithNameStrand

Is there any column in df with name "strand"? If there is, change its name to "strand_old" so that it will conflict with code in other parts of ICAMS package.

StandardChromName

Standardize the chromosome name annotations for a data frame.

TestMakeCatalogFromStrelkaSBSVCFs

This function is to make catalogs from the sample Strelka SBS VCF files to compare with the expected catalog information.

Write a catalog to a file.

RenameColumnsWithNameVAF

Is there any column in df1 with name "VAF"? If there is, change its name to "VAF_old" so that it will conflict with code in other parts of ICAMS package.

TestPlotCatCOMPOSITE

Plot the a SignatureAnalyzer COMPOSITE signature or catalog into separate pdfs

Convert 96-channel mutation-type identifiers like this "ACTA" -> "A[C>A]T".

StopIfRegionIllegal

Stop if region is illegal.

TransRownames.ID.PCAWG.SigPro

For indels, convert ICAMS/PCAWG7 rownames into SigProfiler rownames.

StopIfTranscribedRegionIllegal

Stop if region is illegal for an in-transcript catalogs

TestMakeCatalogFromStrelkaIDVCFs

This function is to make catalogs from the sample Strelka ID VCF files to compare with the expected catalog information.

WriteCatalogIndelSigPro

Write Indel Catalogs in SigProExtractor format.

TestMakeCatalogFromMutectVCFs

This function makes catalogs from the sample Mutect VCF file and compares it with the expected catalog information.

K-mer abundances.

Write a catalog

Reverse complement strings that represent stranded DBSs

Convert 96-channel mutations-type identifiers like this "A[C>A]T" -> "ACTA".

TransRownames.ID.SigPro.PCAWG

For indels, convert SigProfiler rownames into ICAMS/PCAWG7 rownames.

StopIfCatalogTypeIllegal

Stop if catalog.type is illegal.

VCFsToDBSCatalogs

Create DBS catalogs from VCFs

TCFromCouSigCou

Source catalog type is counts or counts.signature

StopIfNrowIllegal

Stop if the number of rows in object is illegal

TCFromDenSigDen

density -> <anything> density.signature -> density.signature, counts.signature

Create a catalog from a matrix, data.frame, or vector.

Reverse complement every string in string.vec.

Add sequence context and transcript information to an in-memory DBS VCF.

Add sequence context and transcript information to an in-memory SBS VCF.

Canonicalize1ID

Given a single insertion or deletion in context categorize it.

CatalogRowOrder

Standard order of row names in a catalog.

Add sequence context to a data frame with mutation records

Canonicalize1INS

Given an insertion and its sequence context, categorize it.

Determine the mutation types of insertions and deletions.

Canonicalize1Del

Given a deletion and its sequence context, categorize it.

Add sequence context to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome.