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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 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

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Version

Install

install.packages('ICAMS')

Monthly Downloads

548

Version

2.0.7

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/steverozen/ICAMS

Maintainer

Steve Rozen

Last Published

July 11th, 2019

Functions in ICAMS (2.0.7)

Canonicalize1DEL

Given a deletion and its sequence context, categorize it.

CollapseCatalog

"Collapse" a catalog.

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.

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

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

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

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

Return the length of microhomology at a deletion.

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.

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.

Read chromosome and position information from a bed format file.

ReadAndSplitStrelkaSBSVCFs

Read and split Strelka SBS VCF files.

Plot position probability matrices (PPM) to a PDF file

Write a catalog to a file.

K-mer abundances.

TCFromCouSigCou

Source catalog type is counts or counts.signature

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

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

StandardChromName

Standardize the chromosome name annotations for a data frame.

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: 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.

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

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

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

Generate all possible k-mers of length k.

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

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

Reverse complement strings that represent stranded SBSs

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 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