ICAMS v2.0.7
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In-depth Characterization and Analysis of Mutational Signatures ('ICAMS')
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>. '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.
Readme
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 development version of ICAMS from GitHub with the R command line:
devtools::install_github("steverozen/ICAMS", ref = "v2.0.7-branch")
Reference manual
https://github.com/steverozen/ICAMS/blob/v2.0.7-branch/data-raw/ICAMS_2.0.7.pdf
Functions in ICAMS
| Name | Description | |
| Canonicalize1DEL | Given a deletion and its sequence context, categorize it. | |
| CollapseCatalog | "Collapse" a catalog. | |
| AddTranscript | Add transcript information to a data frame with mutation records | |
| CheckSeqContextInVCF | Check that the sequence context information is consistent with the value of the column REF. | |
| Canonicalize1INS | Given an insertion and its sequence context, categorize it. | |
| CatalogRowOrder | Standard order of row names in a catalog. | |
| AddAndCheckSequenceID | Add sequence context to a data frame with ID (insertion/deletion) mutation records, and confirm that they match the given reference genome. | |
| CanonicalizeID | Given vectors of insertions and deletions in contexts categorize them. | |
| Canonicalize1ID | Given a single insertion or deletion in context categorize it. | |
| CreateOneColDBSMatrix | Create double base catalog for *one* sample from a Variant Call Format (VCF) file | |
| CreateOneColSBSMatrix | Create the matrix an SBS catalog for *one* sample from an in-memory VCF. | |
| GetStrandedKmerCounts | Generate stranded k-mer abundance from a given genome and gene annotation file | |
| PlotPPM | Plot position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file. | |
| CreateExomeStrandedRanges | Create exome transcriptionally stranded regions | |
| GetGenomeKmerCounts | Generate k-mer abundance from a given genome | |
| PlotCatalogToPdf | Plot catalog to a PDF file. | |
| CreateDinucAbundance | Create dinucleotide abundance | |
| GetSequenceKmerCounts | Generate k-mer abundance from given nucleotide sequences | |
| GetExomeKmerCounts | Generate exome k-mer abundance from a given reference genome | |
| ReadCatalog | Read catalog. | |
| AddSeqContext | Add sequence context to a data frame with mutation records | |
| CreateOnePPMFromSBSVCF | Create position probability matrix (PPM) for *one* sample from a Variant Call Format (VCF) file. | |
| CreateTrinucAbundance | Create trinucleotide abundance | |
| InferAbundance | Infer abundance given a matrix-like object and additional information. | |
| FindDelMH | Return the length of microhomology at a deletion. | |
| ReadMutectVCF | Read in the data lines of a Variant Call Format (VCF) file created by MuTect | |
| ReadStrelkaSBSVCFs | Read Strelka SBS (single base substitutions) VCF files. | |
| CreateOneColIDMatrix | Create one column of the matrix for an indel catalog from *one* in-memory VCF. | |
| ReadMutectVCFs | Read Mutect VCF files. | |
| 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) | |
| InferClassOfCatalogForRead | Infer the class of catalog in a file. | |
| CreatePPMFromSBSVCFs | Create position probability matrices (PPM) from a list of SBS vcfs | |
| CreateTetranucAbundance | Create tetranucleotide abundance | |
| ReadAndSplitMutectVCFs | Read and split Mutect VCF files. | |
| ReadBedRanges | Read chromosome and position information from a bed format file. | |
| ReadAndSplitStrelkaSBSVCFs | Read and split Strelka SBS VCF files. | |
| PlotPPMToPdf | Plot position probability matrices (PPM) to a PDF file | |
| WriteCat | Write a catalog to a file. | |
| all.abundance | K-mer abundances. | |
| TCFromCouSigCou | Source catalog type is counts or counts.signature | |
| WriteCatalog | Write a catalog | |
| TCFromDenSigDen | density -> <anything> density.signature -> density.signature, counts.signature | |
| CreateTransRanges | Create a transcript range file from the raw GFF3 File | |
| SplitStrelkaSBSVCF | Split an in-memory Strelka VCF into SBS, DBS, and variants involving > 2 consecutive bases | |
| GetVAF | Extract the VAFs (variant allele frequencies) from a VCF file. | |
| StandardChromName | Standardize the chromosome name annotations for a data frame. | |
| revc | 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. | |
| StopIfRegionIllegal | Stop if region is illegal. | |
| ReadDukeNUSCat192 | Read a 192-channel spectra (or signature) catalog in Duke-NUS format. | |
| StopIfTranscribedRegionIllegal | Stop if region is illegal for an in-transcript catalogs | |
| TranscriptRanges | Transcript ranges data | |
| StopIfCatalogTypeIllegal | Stop if catalog.type is illegal. | |
| StopIfNrowIllegal | 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 | |
| FindMaxRepeatDel | Return the number of repeat units in which a deletion is embedded. | |
| CreatePentanucAbundance | Create pentanucleotide abundance | |
| FindMaxRepeatIns | Return the number of repeat units in which an insertion is embedded. | |
| ReadStrelkaIDVCFs | Read Strelka ID (insertion and deletion) VCF files. | |
| MutectVCFFilesToCatalog | Create SBS, DBS and Indel catalogs from Mutect VCF files | |
| ICAMS | 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 | |
| ReadStrelkaSBSVCF | Read in the data lines of an SBS VCF created by Strelka version 1 | |
| GenerateEmptyKmerCounts | Generate an empty matrix of k-mer abundance | |
| RemoveRangesOnBothStrand | 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. | |
| as.catalog | 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 | |
| IsGRCh37 | Test if object is BSgenome.Hsapiens.1000genome.hs37d5. | |
| IsGRCm38 | Test if object is BSgenome.Mmusculus.UCSC.mm10. | |
| GenerateKmer | Generate all possible k-mers of length k. | |
| IsGRCh38 | Test if object is BSgenome.Hsapiens.UCSC.hg38. | |
| NormalizeGenomeArg | Take strings representing a genome and return the BSgenome object. | |
| MakeDataFrameFromStrelkaSBSVCF | Read in the data lines of an SBS VCF created by Strelka version 1 | |
| RevcDBS144 | 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 | |
| RevcSBS96 | Reverse complement strings that represent stranded SBSs | |
| PlotCatalog | Plot one spectrum or signature. | |
| SplitListOfMutectVCFs | 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 | MakeVCFDBSdf Take DBS ranges and the original VCF and generate a VCF with dinucleotide REF and ALT alleles. | |
| ReadStapleGT96SBS | Read a 96-channel spectra (or signature) catalog where rownames are e.g. "A[C>A]T" | |
| ReadStrelkaIDVCF | Read in the data lines of an ID VCF created by Strelka version 1 | |
| SplitOneMutectVCF | 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 | |
| VCFsToIDCatalogs | Create ID (insertion and deletion) catalog from ID VCFs | |
| VCFsToSBSCatalogs | Create SBS catalogs from SBS VCFs | |
| TransformCatalog | Transform between counts and density spectrum catalogs and counts and density signature catalogs. | |
| VCFsToDBSCatalogs | Create DBS catalogs from VCFs | |
| No Results! | ||
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Details
| Type | Package |
| License | GPL-3 |
| URL | https://github.com/steverozen/ICAMS |
| BugReports | https://github.com/steverozen/ICAMS/issues |
| Encoding | UTF-8 |
| LazyData | true |
| Language | en-US |
| biocViews | |
| RoxygenNote | 6.1.1 |
| NeedsCompilation | no |
| Packaged | 2019-07-08 03:20:22 UTC; steve |
| Repository | CRAN |
| Date/Publication | 2019-07-11 12:53:11 UTC |
| depends | , R (>= 3.5) |
| imports | Biostrings , BSgenome , BSgenome.Hsapiens.1000genomes.hs37d5 , BSgenome.Hsapiens.UCSC.hg38 , data.table , dplyr , GenomeInfoDb , GenomicRanges , graphics , grDevices , IRanges , RColorBrewer , stats , stringi , utils |
| suggests | BSgenome.Mmusculus.UCSC.mm10 , testthat |
| Contributors | Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu |
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