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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_2.1.2.pdf

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Version

Install

install.packages('ICAMS')

Monthly Downloads

563

Version

2.1.2

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/steverozen/ICAMS

Maintainer

Steve Rozen

Last Published

April 21st, 2020

Functions in ICAMS (2.1.2)

CollapseCatalog

"Collapse" a catalog.

CreateTransRanges

Create a transcript range file from the raw GFF3 File

CreateTrinucAbundance

Create trinucleotide abundance

CheckSeqContextInVCF

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

CatalogRowOrder

Standard order of row names in a catalog.

CreateExomeStrandedRanges

Create exome transcriptionally stranded regions

CreateOneColDBSMatrix

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

CheckAndReorderRownames

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

CreateStrandedTrinucAbundance

Create stranded trinucleotide abundance

CheckAndFixChrNames

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

CreateTetranucAbundance

Create tetranucleotide abundance

CreateDinucAbundance

Create dinucleotide abundance

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

CreateOnePPMFromSBSVCF

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

GetMutationLoadsFromMutectVCFs

Get mutation loads information from Mutect VCF files.

GetCustomKmerCounts

Generate custom k-mer abundance from a given reference genome

CreatePentanucAbundance

Create pentanucleotide abundance

Canonicalize1INS

Given an insertion and its sequence context, categorize it.

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

GetMutationLoadsFromStrelkaIDVCFs

Get mutation loads information from Strelka ID VCF files.

GetGenomeKmerCounts

Generate k-mer abundance from a given genome

CreateStrandedDinucAbundance

Create stranded dinucleotide abundance

GenerateEmptyKmerCounts

Generate an empty matrix of k-mer abundance

Determine the mutation types of insertions and deletions.

CreatePPMFromSBSVCFs

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

CreateOneColSBSMatrix

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

Return the length of microhomology at a deletion.

CreateOneColIDMatrix

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

FindMaxRepeatIns

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

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

GetStrandedKmerCounts

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

MutectVCFFilesToCatalog

Create SBS, DBS and Indel catalogs from Mutect VCF files

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

Generate all possible k-mers of length k.

GetSequenceKmerCounts

Generate k-mer abundance from given nucleotide sequences

GetMutationLoadsFromStrelkaSBSVCFs

Get mutation loads information from Strelka SBS VCF files.

FindMaxRepeatDel

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

GeneExpressionData

Example gene expression data from two cell lines.

Read chromosome and position information from a bed format file.

ICAMS: In-depth Characterization and Analysis of Mutational Signatures

InferClassOfCatalogForRead

Infer the class of catalog in a file.

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

ReadStrelkaSBSVCF

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

ReadStrelkaSBSVCFs

Read Strelka SBS (single base substitutions) VCF files.

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

ReadDukeNUSCat192

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

MutectVCFFilesToCatalogAndPlotToPdf

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

MakeDataFrameFromMutectVCF

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

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.

MutectVCFFilesToZipFile

Create a zip file which contains catalogs and plot PDFs from Mutect VCF files

Plot position probability matrices (PPM) to a PDF file

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

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

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

Extract the VAFs (variant allele frequencies) and read depth information from a VCF file.

Plot one spectrum or signature.

Plot96PartOfCompositeToPDF

Plot the SBS96 part of a SignatureAnalyzer COMPOSITE signature or catalog

NormalizeGenomeArg

Take strings representing a genome and return the BSgenome object.

ReadAndSplitStrelkaSBSVCFs

Read and split Strelka SBS VCF files.

ReadAndSplitMutectVCFs

Read and split Mutect VCF files.

ReadStrelkaIDVCFs

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

ReadStrelkaIDVCF

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

StopIfRegionIllegal

Stop if region is illegal.

SplitListOfStrelkaSBSVCFs

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

PlotCatalogToPdf

Plot catalog to a PDF file.

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

TestMakeCatalogFromStrelkaSBSVCFs

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

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.

SplitOneMutectVCF

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

Write a catalog

Write a catalog to a file.

MakeDataFrameFromStrelkaSBSVCF

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

Read Mutect VCF files.

StrelkaSBSVCFFilesToCatalog

Create SBS and DBS catalogs from Strelka SBS VCF files.

MakeDataFrameFromVCF

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

StrelkaIDVCFFilesToZipFile

Create a zip file which contains ID (small insertion and deletion) catalog and plot PDF from Strelka ID VCF files

TestPlotCatCOMPOSITE

Plot the a SignatureAnalyzer COMPOSITE signature or catalog into separate pdfs

StopIfTranscribedRegionIllegal

Stop if region is illegal for an in-transcript catalogs

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.

SplitStrelkaSBSVCF

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

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)

TranscriptRanges

Transcript ranges data

StopIfCatalogTypeIllegal

Stop if catalog.type is illegal.

VCFsToIDCatalogs

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

StandardChromName

Standardize the chromosome name annotations for a data frame.

StrelkaSBSVCFFilesToZipFile

Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF files

StrelkaSBSVCFFilesToCatalogAndPlotToPdf

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

TCFromDenSigDen

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

VCFsToSBSCatalogs

Create SBS catalogs from SBS VCFs

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

TransRownames.ID.PCAWG.SigPro

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

ReadStapleGT96SBS

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

TransformCatalog

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

StopIfNrowIllegal

Stop if the number of rows in object is illegal

Reverse complement every string in string.vec.

Reverse complement strings that represent stranded DBSs

TransRownames.ID.SigPro.PCAWG

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

RemoveRangesOnBothStrand

Remove ranges that fall on both strands

TCFromCouSigCou

Source catalog type is counts or counts.signature

Reverse complement strings that represent stranded SBSs

WriteCatalogIndelSigPro

Write Indel Catalogs in SigProExtractor format.

SplitListOfMutectVCFs

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

K-mer abundances.

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

TestMakeCatalogFromMutectVCFs

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

TestMakeCatalogFromStrelkaIDVCFs

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

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

VCFsToDBSCatalogs

Create DBS catalogs from VCFs

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

Canonicalize1ID

Given a single insertion or deletion in context categorize it.

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

Canonicalize1Del

Given a deletion and its sequence context, categorize it.

CalBaseCountsFrom3MerAbundance

Calculate base counts from three mer abundance

AddRunInformation

Create a run information text file from generating zip archive from VCF files.

Add transcript information to a data frame with mutation records

CalculateNumberOfSpace

Calculate the number of space needed to add strand bias statistics to the run-information.txt file.

Add sequence context to a data frame with mutation records