Create dinucleotide abundance
Add transcript information to a data frame with mutation records
Create one column of the matrix for an indel catalog from *one* in-memory VCF.
Create the matrix a DBS catalog for *one* sample from an in-memory VCF.
Return the number of repeat units in which a deletion is embedded.
Generate stranded k-mer abundance from a given genome and gene annotation file
Check that the sequence context information is consistent with the value of
the column REF.
Create tetranucleotide abundance
Check and, if possible, correct the chromosome names in a VCF data.frame.
Create a transcript range file from the raw GFF3 File
Check whether the rownames of object are correct, if yes then put the
rows in the correct order.
"Collapse" a catalog.
MakeDataFrameFromStrelkaSBSVCF
Read in the data lines of an SBS VCF created by Strelka version 1
Plot position probability matrix (PPM) for *one* sample from a Variant Call Format
(VCF) file.
MakeVCFDBSdf Take DBS ranges and the original VCF and generate a VCF with
dinucleotide REF and ALT alleles.
Extract the VAFs (variant allele frequencies) from a VCF file.
CreateStrandedDinucAbundance
Create stranded dinucleotide abundance
Return the number of repeat units in which an insertion
is embedded.
Example gene expression data from two cell lines.
CreateStrandedTrinucAbundance
Create stranded trinucleotide abundance
ICAMS: In-depth Characterization and Analysis of Mutational Signatures
Return the length of microhomology at a deletion.
InferClassOfCatalogForRead
Infer the class of catalog in a file.
Create trinucleotide abundance
CreateExomeStrandedRanges
Create exome transcriptionally stranded regions
Generate k-mer abundance from given nucleotide sequences
Infer abundance given a matrix-like object and additional information.
Generate k-mer abundance from a given genome
Infer the correct rownames for a matrix based on its number of rows
Plot one spectrum or signature.
Plot96PartOfCompositeToPDF
Plot the SBS96 part of a SignatureAnalyzer COMPOSITE signature or catalog
Create position probability matrices (PPM) from a list of SBS vcfs
MutectVCFFilesToCatalogAndPlotToPdf
Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF
Create position probability matrix (PPM) for *one* sample from
a Variant Call Format (VCF) file.
Create pentanucleotide abundance
Generate exome k-mer abundance from a given reference genome
Generate all possible k-mers of length k.
Create the matrix an SBS catalog for *one* sample from an in-memory VCF.
Create SBS, DBS and Indel catalogs from Mutect VCF files
Take strings representing a genome and return the BSgenome Generate an empty matrix of k-mer abundance
Remove ranges that fall on both strands
Create ID (small insertion and deletion) catalog from ID VCFs
StrelkaIDVCFFilesToCatalog
Create ID (small insertion and deletion) catalog from Strelka ID VCF files
Read a 192-channel spectra (or signature) catalog in Duke-NUS format.
Transcript ranges data
Transform between counts and density spectrum catalogs
and counts and density signature catalogs.
StrelkaIDVCFFilesToCatalogAndPlotToPdf
Create ID (small insertion and deletion) catalog from Strelka ID VCF files
and plot them to PDF
Plot catalog to a PDF file.
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 created by
Mutect
Create SBS catalogs from SBS VCFs
ReadAndSplitStrelkaSBSVCFs
Read and split Strelka SBS VCF files.
Read Strelka ID (small insertion and deletion) VCF files.
Split a mutect2 VCF into SBS, DBS, and ID VCFs, plus a list of other mutations
MakeDataFrameFromMutectVCF
Read in the data lines of a Variant Call Format (VCF) file created by Mutect
Plot position probability matrices (PPM) to a PDF file
Test if object is BSgenome.Mmusculus.UCSC.mm10.
Read and split Mutect VCF files.
SplitListOfStrelkaSBSVCFs
Split a list of in-memory Strelka SBS VCF into SBS, DBS, and variants involving
> 2 consecutive bases
Read in the data lines of an ID VCF created by Strelka version 1
Read in the data lines of an SBS VCF created by Strelka version 1
Test if object is BSgenome.Hsapiens.1000genome.hs37d5.
Test if object is BSgenome.Hsapiens.UCSC.hg38.
Read Strelka SBS (single base substitutions) VCF files.
Plot transcription strand bias with respect to gene expression values.
Read a 96-channel spectra (or signature) catalog where rownames are e.g. "A[C>A]T".
Split each Mutect VCF into SBS, DBS, and ID VCFs (plus two
VCF-like data frame with left-over rows).
Read Mutect VCF files.
Reverse complement strings that represent stranded SBSs
PlotTransBiasGeneExpToPdf
Plot transcription strand bias with respect to gene expression values to a
PDF file.
StrelkaSBSVCFFilesToCatalog
Create SBS and DBS catalogs from Strelka SBS VCF files.
Split an in-memory Strelka VCF into SBS, DBS, and variants involving
> 2 consecutive bases
StrelkaSBSVCFFilesToCatalogAndPlotToPdf
Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF
Read chromosome and position information from a bed format file.
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.
Read catalog.
Standardize the chromosome name annotations for a data frame.
TestMakeCatalogFromStrelkaSBSVCFs
This function is to make catalogs from the sample Strelka SBS VCF files
to compare with the expected catalog information.
Write a catalog to a file.
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.
Plot the a SignatureAnalyzer COMPOSITE signature or catalog into separate pdfs
Convert 96-channel mutation-type identifiers like this "ACTA" -> "A[C>A]T".
Stop if region is illegal.
TransRownames.ID.PCAWG.SigPro
For indels, convert ICAMS/PCAWG7 rownames into SigProfiler rownames.
StopIfTranscribedRegionIllegal
Stop if region is illegal for an in-transcript catalogs
TestMakeCatalogFromStrelkaIDVCFs
This function is to make catalogs from the sample Strelka ID VCF files
to compare with the expected catalog information.
Write Indel Catalogs in SigProExtractor format.
TestMakeCatalogFromMutectVCFs
This function makes catalogs from the sample Mutect VCF file
and compares it with the expected catalog information.
K-mer abundances.
Write a catalog
Reverse complement strings that represent stranded DBSs
Convert 96-channel mutations-type identifiers like this "A[C>A]T" -> "ACTA".
TransRownames.ID.SigPro.PCAWG
For indels, convert SigProfiler rownames into ICAMS/PCAWG7 rownames.
Stop if catalog.type is illegal.
Create DBS catalogs from VCFs
Source catalog type is counts or counts.signature
Stop if the number of rows in object is illegal
density -> <anything>
density.signature -> density.signature, counts.signature
Create a catalog from a matrix, data.frame, or vector.
Reverse complement every string in string.vec.
Add sequence context and transcript information to an in-memory DBS VCF.
Add sequence context and transcript information to an in-memory SBS VCF.
Given a single insertion or deletion in context categorize it.
Standard order of row names in a catalog.
Add sequence context to a data frame with mutation records
Given an insertion and its sequence context, categorize it.
Determine the mutation types of insertions and deletions.
Given a deletion and its sequence context, categorize it.
Add sequence context to an in-memory ID (insertion/deletion) VCF, and
confirm that they match the given reference genome.