ICAMS

Add and check DBS class in an annotated VCF with the corresponding DBS mutation matrix

Add and check SBS class in an annotated VCF with the corresponding SBS mutation matrix

Add DBS mutation class to an annotated DBS VCF

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

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 VCF

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

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

Calculate base counts from three mer abundance

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

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.frame.

Check and, if possible, correct the chromosome names in a trans.ranges data.table

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

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 matrix

Check SBS mutation class in VCF with the corresponding SBS mutation matrix

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

"Collapse" a catalog

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-memory VCF.

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

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

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

Create pentanucleotide abundance

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.

Analogous to GetMutectVAF, calculating VAF and read depth from PCAWG7 consensus vcfs

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 annotation file

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

ICAMS: In-depth Characterization and Analysis of Mutational Signatures

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

These two functions is applicable only for internal ICAMS-formatted catalog object.

This function converts an data.table imported from external catalog text file into ICAMS internal catalog object of appropriate type.

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.

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

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

Create SBS, DBS and Indel catalogs from Mutect VCF files

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

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

Take strings representing a genome and return the BSgenome object.

Plot the SBS96 part of a SignatureAnalyzer COMPOSITE signature or catalog

Plot one spectrum or signature

Plot catalog to a PDF file

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

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 to a PDF file

Read and split Mutect VCF files

Read and split Strelka SBS VCF files

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 read catalog

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 Mutect

Read Mutect VCF files.

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

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

Read Strelka ID (small insertion and deletion) VCF files

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. 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

Read VCF files

Remove ranges that fall on both strands

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.

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.

Convert 1536-channel mutation-type identifiers like this "ACCGTA" -> "AC[C>A]GT"

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

Reverse complement strings that represent stranded DBSs

Reverse complement strings that represent stranded SBSs

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

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

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

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

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 involving > 2 consecutive bases

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

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

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

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

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

Create SBS and DBS catalogs from Strelka SBS VCF files

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

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

Source catalog type is counts or counts.signature

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

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

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

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

Plot the a SignatureAnalyzer COMPOSITE signature or catalog into separate pdfs

For indels, convert ICAMS/PCAWG7 rownames into SigProfiler rownames

For indels, convert SigProfiler rownames into ICAMS/PCAWG7 rownames

Transcript ranges data

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

Convert SBS1536-channel mutations-type identifiers like this "AC[C>A]GT" -> "ACCGTA"

Convert DBS78-channel mutations-type identifiers like this "AC>GA" -> "ACGA"

Convert SBS96-channel mutations-type identifiers like this "A[C>A]T" -> "ACTA"

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 insertion and deletion) 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 in the zip archive.

Write a catalog to a file.

Write a catalog

Write Indel Catalogs in SigProExtractor format

K-mer abundances

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

Reverse complement every string in string.vec