In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
Add and check DBS class in an annotated VCF with the corresponding DBS...
Add and check SBS class in an annotated VCF with the corresponding SBS...
Add DBS mutation class to an annotated DBS VCF
Create a run information text file from generating zip archive from VC...
Add SBS mutation class to an annotated SBS VCF
Add sequence context to a data frame with mutation records
Add transcript information to a data frame with mutation records
Add sequence context and transcript information to an in-memory DBS VC...
Add sequence context and transcript information to an in-memory ID (in...
Add sequence context and transcript information to an in-memory SBS VC...
Create a catalog from a matrix, data.frame, or vector
Calculate base counts from three mer abundance
Calculate the number of space needed to add strand bias statistics to ...
Given a deletion and its sequence context, categorize it
Given a single insertion or deletion in context categorize it.
Given an insertion and its sequence context, categorize it.
Determine the mutation types of insertions and deletions.
Standard order of row names in a catalog
Check and, if possible, correct the chromosome names in a VCF `data.fr...
Check and, if possible, correct the chromosome names in a trans.ranges...
Check whether the rownames of object are correct, if yes then put th...
Check and return DBS catalogs
Check and return the DBS mutation matrix
Check and return ID catalog
Check and return the ID mutation matrix
Check and return SBS catalogs
Check and return the SBS mutation matrix
Check DBS mutation class in VCF with the corresponding DBS mutation ma...
Check SBS mutation class in VCF with the corresponding SBS mutation ma...
Check that the sequence context information is consistent with the val...
"Collapse" a catalog
Covert an ICAMS Catalog to SigProfiler format
Covert an ICAMS SBS96 Catalog to SigProfiler format
Create dinucleotide abundance
Create exome transcriptionally stranded regions
Create the matrix a DBS catalog for one sample from an in-memory VCF...
Create one column of the matrix for an indel catalog from one in-mem...
Create the matrix an SBS catalog for one sample from an in-memory VC...
Create position probability matrix (PPM) for one sample from a Varia...
Create pentanucleotide abundance
Create position probability matrices (PPM) from a list of SBS vcfs
Create stranded dinucleotide abundance
Create stranded trinucleotide abundance
Create tetranucleotide abundance
Create a transcript range file from the raw GFF3 File
Create trinucleotide abundance
Return the length of microhomology at a deletion
Return the number of repeat units in which a deletion is embedded
Return the number of repeat units in which an insertion is embedded.
Example gene expression data from two cell lines
Generate an empty matrix of k-mer abundance
Generate all possible k-mers of length k.
Generate PFMmatrix (Position Frequency Matrix) from a given list of se...
Generate reconstructed VCFs from indel (small insertions and deletions...
Generate reconstructed VCFs from indel (small insertions and deletions...
Get all the sequence contexts of the indels in a given 1 base-pair ind...
Generate custom k-mer abundance from a given reference genome
Generate k-mer abundance from a given genome
Get mutation loads information from Mutect VCF files.
Get mutation loads information from Strelka ID VCF files.
Get mutation loads information from Strelka SBS VCF files.
Generate k-mer abundance from given nucleotide sequences
Generate stranded k-mer abundance from a given genome and gene annotat...
Extract the VAFs (variant allele frequencies) and read depth informati...
Generate Haplotype plot from a given list of sequences
ICAMS: In-depth Characterization and Analysis of Mutational Signatures
Infer abundance given a matrix-like object and additional informat...
These two functions is applicable only for internal ICAMS-formatted ca...
This function converts an data.table imported from external catalog te...
Infer reference genome name from a character string
Infer the correct rownames for a matrix based on its number of rows
Test if object is BSgenome.Hsapiens.1000genome.hs37d5.
Test if object is BSgenome.Hsapiens.UCSC.hg38.
Test if object is BSgenome.Mmusculus.UCSC.mm10.
Check whether an R object contains one of the ICAMS catalog classes
Check whether the BSgenome package is installed
Read in the data lines of a Variant Call Format (VCF) file
MakeVCFDBSdf Take DBS ranges and the original VCF and generate a VCF w...
[Deprecated, use VCFsToCatalogs(variant.caller = "mutect") instead]Cre...
[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "mutect")...
[Deprecated, use VCFsToZipFile(variant.caller = "mutect") instead]Crea...
Take strings representing a genome and return the BSgenome object.
Plot the SBS96 part of a SignatureAnalyzer COMPOSITE signature or cata...
Plot one spectrum or signature
Plot catalog to a PDF file
Generate dot-line plot for sequence contest of 1bp indel
Plot position probability matrix (PPM) for one sample from a Variant...
Plot position probability matrices (PPM) to a PDF file
Plot transcription strand bias with respect to gene expression values
Plot transcription strand bias with respect to gene expression values ...
[Deprecated, use ReadAndSplitVCFs(variant.caller = "mutect") instead]R...
[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]...
Read and split VCF files
Read chromosome and position information from a bed format file.
Read catalog
Get error message and either stop or create a null error output for re...
Internal read catalog function to be wrapped in a tryCatch
Read a 192-channel spectra (or signature) catalog in Duke-NUS format
Read in the data lines of a Variant Call Format (VCF) file created by ...
Read Mutect VCF files.
Read a 96-channel spectra (or signature) catalog where rownames are e....
Read in the data lines of an ID VCF created by Strelka version 1
[Deprecated, use ReadAndSplitVCFs(variant.caller = "strelka") instead]...
Read in the data lines of an SBS VCF created by Strelka version 1
Read Strelka SBS (single base substitutions) VCF files.
Read transcript ranges and strand information from a gff3 format file....
Read in the data lines of a Variant Call Format (VCF) file
Read VCF files
Remove ranges that fall on both strands
Is there any column in df with name "end"? If there is, change its n...
Is there any column in df with name "start"? If there is, change its...
Is there any column in df with name "strand"? If there is, change it...
Is there any column in df with name "VAF"? If there is, change its n...
Convert 1536-channel mutation-type identifiers like this `"ACCGTA" -> ...
Convert 96-channel mutation-type identifiers like this `"ACTA" -> "A[C...
Reverse complement every string in string.vec
Reverse complement strings that represent stranded DBSs
Reverse complement strings that represent stranded SBSs
Select variants according to chromosome names specified by user
Read a VCF file into a data frame with minimal processing.
Split each Mutect VCF into SBS, DBS, and ID VCFs (plus VCF-like data f...
Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants ...
Split each VCF into SBS, DBS, and ID VCFs (plus VCF-like data frame wi...
Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other m...
Split a VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
Split an in-memory SBS VCF into pure SBSs, pure DBSs, and variants inv...
Split an in-memory Strelka VCF into SBS, DBS, and variants involving >...
Standardize the chromosome name annotations for a data frame.
Standardize the chromosome name annotations for a data frame.
Stop if catalog.type is illegal.
Stop if the number of rows in object is illegal
Stop if region is illegal.
Stop if region is illegal for an in-transcript catalogs
[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]Cr...
[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka"...
[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]Cre...
[Deprecated, use VCFsToCatalogs(variant.caller = "strelka") instead]Cr...
[Deprecated, use VCFsToCatalogsAndPlotToPdf(variant.caller = "strelka"...
[Deprecated, use VCFsToZipFile(variant.caller = "strelka") instead]Cre...
Get all the sequence contexts of the indels in a given 1 base-pair ind...
Source catalog type is counts or counts.signature
density -> <anything> density.signature -> density.signature, counts.s...
This function makes catalogs from the sample Mutect VCF file and compa...
This function is to make catalogs from the sample Strelka ID VCF files...
This function is to make catalogs from the sample Strelka SBS VCF file...
Plot the a SignatureAnalyzer COMPOSITE signature or catalog into separ...
Transcript ranges data
Transform between counts and density spectrum catalogs and counts and ...
For indels, convert ICAMS/PCAWG7 rownames into SigProfiler rownames
For indels, convert SigProfiler rownames into ICAMS/PCAWG7 rownames
Convert SBS1536-channel mutations-type identifiers like this `"AC[C>A]...
Convert DBS78-channel mutations-type identifiers like this `"AC>GA" ->...
Convert SBS96-channel mutations-type identifiers like this `"A[C>A]T" ...
Create SBS, DBS and Indel catalogs from VCFs
Create SBS, DBS and Indel catalogs from VCFs and plot them to PDF
Create DBS catalogs from VCFs
Create ID (small insertions and deletions) catalog from ID VCFs
Create SBS catalogs from SBS VCFs
Create a zip file which contains catalogs and plot PDFs from VCFs
Analogous to VCFsToZipFile, also generates density CSV and PDF files...
Write a catalog to a file.
Write a catalog
Write Indel Catalogs in SigProExtractor format
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> and "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types", Genome Research 2020 <doi:10.1101/gr.255620.119>. '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" (i.e. representation as mutations per megabase) mutational spectra or signatures.