Given a deletion and its sequence context, categorize it.
"Collapse" a catalog.
Add transcript information to a data frame with mutation records
Check that the sequence context information is consistent with the value of
the column REF.
Given an insertion and its sequence context, categorize it.
Standard order of row names in a catalog.
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.
Given a single insertion or deletion in context categorize it.
Create double base catalog for *one* sample from
a Variant Call Format (VCF) file
Create the matrix an SBS catalog for *one* sample from an in-memory VCF.
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
Generate k-mer abundance from a given genome
Plot catalog to a PDF file.
Create dinucleotide abundance
Generate k-mer abundance from given nucleotide sequences
Generate exome k-mer abundance from a given reference genome
Read catalog.
Add sequence context to a data frame with mutation records
Create position probability matrix (PPM) for *one* sample from
a Variant Call Format (VCF) file.
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
Read Strelka SBS (single base substitutions) VCF files.
Create one column of the matrix for an indel catalog from *one* in-memory VCF.
Read Mutect 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)
InferClassOfCatalogForRead
Infer the class of catalog in a file.
Create position probability matrices (PPM) from a list of SBS vcfs
Create tetranucleotide abundance
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.
Source catalog type is counts or counts.signature
Write a catalog
density -> <anything>
density.signature -> density.signature, counts.signature
Create a transcript range file from the raw GFF3 File
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.
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.
Stop if region is illegal.
Read a 192-channel spectra (or signature) catalog in Duke-NUS format.
StopIfTranscribedRegionIllegal
Stop if region is illegal for an in-transcript catalogs
Transcript ranges data
Stop if catalog.type is illegal.
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
Return the number of repeat units in which a deletion
is embedded.
Create pentanucleotide abundance
Return the number of repeat units in which an insertion
is embedded.
Read Strelka ID (insertion and deletion) VCF files.
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
Read in the data lines of an SBS VCF created by Strelka version 1
Generate an empty matrix of k-mer abundance
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.
Take strings representing a genome and return the BSgenome 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.
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.
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
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
Create ID (insertion and deletion) catalog from ID VCFs
Create SBS catalogs from SBS VCFs
Transform between counts and density spectrum catalogs
and counts and density signature catalogs.
Create DBS catalogs from VCFs