ICAMS: AnnotateIDVCF – R documentation

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AnnotateIDVCF

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

Description

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

Usage

AnnotateIDVCF(
  ID.vcf,
  ref.genome,
  flag.mismatches = 0,
  name.of.VCF = NULL,
  suppress.discarded.variants.warnings = TRUE
)

Arguments

`ID.vcf`	An in-memory ID (insertion/deletion) VCF as a `data.frame`. This function expects that there is a "context base" to the left, for example REF = ACG, ALT = A (deletion of CG) or REF = A, ALT = ACC (insertion of CC).
`ref.genome`	A `ref.genome` argument as described in `ICAMS`.
`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. See element `discarded.variants` in the return value for more details.
`name.of.VCF`	Name of the VCF file.
`suppress.discarded.variants.warnings`	Logical. Whether to suppress warning messages showing information about the discarded variants. Default is TRUE.

Value

A list of elements:

annotated.vcf: The original VCF data frame with two new columns added to the input data frame:
- seq.context: The sequence embedding the variant.
- seq.context.width: The width of seq.context to the left.
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.

Examples

file <- c(system.file("extdata/Strelka-ID-vcf/",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMS"))
ID.vcf <- ReadStrelkaIDVCFs(file)[[1]]
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  list <- AnnotateIDVCF(ID.vcf, ref.genome = "hg19")
  annotated.ID.vcf <- list$annotated.vcf}

ICAMS

In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release