MutectVCFFilesToCatalogAndPlotToPdf: Create SBS, DBS and Indel catalogs from Mutect VCF files and...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Details Value ID classification Note Comments Examples

Create 3 SBS catalogs (96, 192, 1536), 3 DBS catalogs (78, 136, 144) and Indel catalog from the Mutect VCFs specified by files and plot them to PDF

MutectVCFFilesToCatalogAndPlotToPdf(
  files,
  ref.genome,
  trans.ranges = NULL,
  region = "unknown",
  names.of.VCFs = NULL,
  tumor.col.names = NA,
  output.file = "",
  flag.mismatches = 0,
  return.annotated.vcfs = FALSE,
  suppress.discarded.variants.warnings = TRUE
)

`files`	Character vector of file paths to the Mutect VCF files.
`ref.genome`	A `ref.genome` argument as described in `ICAMS`.
`trans.ranges`	Optional. If `ref.genome` specifies one of the `BSgenome` object `BSgenome.Hsapiens.1000genomes.hs37d5` `BSgenome.Hsapiens.UCSC.hg38` `BSgenome.Mmusculus.UCSC.mm10` then the function will infer `trans.ranges` automatically. Otherwise, user will need to provide the necessary `trans.ranges`. Please refer to `TranscriptRanges` for more details. If `is.null(trans.ranges)` do not add transcript range information.
`region`	A character string designating a genomic region; see `as.catalog` and `ICAMS`.
`names.of.VCFs`	Optional. Character vector of names of the VCF files. The order of names in `names.of.VCFs` should match the order of VCF file paths in `files`. If `NULL`(default), this function will remove all of the path up to and including the last path separator (if any) in `files` and file paths without extensions (and the leading dot) will be used as the names of the VCF files.
`tumor.col.names`	Optional. Character vector of column names in VCFs which contain the tumor sample information. The order of names in `tumor.col.names` should match the order of VCFs specified in `files`. If `tumor.col.names` is equal to `NA`(default), this function will use the 10th column in all the VCFs to calculate VAFs. See `GetMutectVAF` for more details.
`output.file`	Optional. The base name of the PDF files to be produced; multiple files will be generated, each ending in x`.pdf`, where x indicates the type of catalog plotted in the file.
`flag.mismatches`	Deprecated. If there are ID variants whose `REF` do not match the extracted sequence from `ref.genome`, the function will automatically discard these variants and an element `discarded.variants` will appear in the return value. See `AnnotateIDVCF` for more details.
`return.annotated.vcfs`	Logical. Whether to return the annotated VCFs with additional columns showing mutation class for each variant. Default is FALSE.
`suppress.discarded.variants.warnings`	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

This function calls MutectVCFFilesToCatalog and PlotCatalogToPdf

A list containing the following objects:

catSBS96, catSBS192, catSBS1536: Matrix of 3 SBS catalogs (one each for 96, 192, and 1536).
catDBS78, catDBS136, catDBS144: Matrix of 3 DBS catalogs (one each for 78, 136, and 144).
catID: Matrix of ID (small insertion and deletion) catalog.
discarded.variants: Non-NULL only if there are variants that were excluded from the analysis. See the added extra column discarded.reason for more details.
annotated.vcfs: Non-NULL only if return.annotated.vcfs = TRUE. A list of elements:
- SBS: SBS VCF annotated by AnnotateSBSVCF with three new columns SBS96.class, SBS192.class and SBS1536.class showing the mutation class for each SBS variant.
- DBS: DBS VCF annotated by AnnotateDBSVCF with three new columns DBS78.class, DBS136.class and DBS144.class showing the mutation class for each DBS variant.
- ID: ID VCF annotated by AnnotateIDVCF with one new column ID.class showing the mutation class for each ID variant.

If trans.ranges is not provided by user and cannot be inferred by ICAMS, SBS 192 and DBS 144 catalog will not be generated. Each catalog has attributes added. See as.catalog for more details.

See https://github.com/steverozen/ICAMS/raw/master/data-raw/PCAWG7_indel_classification_2017_12_08.xlsx for additional information on ID (small insertion and deletion) mutation classification.

See the documentation for Canonicalize1Del which first handles deletions in homopolymers, then handles deletions in simple repeats with longer repeat units, (e.g. CACACACA, see FindMaxRepeatDel), and if the deletion is not in a simple repeat, looks for microhomology (see FindDelMH).

See the code for unexported function CanonicalizeID and the functions it calls for handling of insertions.

SBS 192 and DBS 144 catalogs include only mutations in transcribed regions. In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

To add or change attributes of the catalog, you can use function attr.
For example, attr(catalog, "abundance") <- custom.abundance.

file <- c(system.file("extdata/Mutect-vcf",
                      "Mutect.GRCh37.s1.vcf",
                      package = "ICAMS"))
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catalogs <-
    MutectVCFFilesToCatalogAndPlotToPdf(file, ref.genome = "hg19",
                                        trans.ranges = trans.ranges.GRCh37,
                                        region = "genome",
                                        output.file =
                                        file.path(tempdir(), "Mutect"))}