CreateOneColIDMatrix: Create one column of the matrix for an indel catalog from...

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

Create one column of the matrix for an indel catalog from *one* in-memory VCF.

Description

Create one column of the matrix for an indel catalog from *one* in-memory VCF.

Usage

CreateOneColIDMatrix(
  ID.vcf,
  SBS.vcf = NULL,
  sample.id = "count",
  return.annotated.vcf = FALSE
)

Arguments

ID.vcf	An in-memory VCF as a data.frame annotated by the AnnotateIDVCF function. It must only contain indels and must not contain SBSs (single base substitutions), DBSs, or triplet base substitutions, etc. One design decision for variant callers is the representation of "complex indels", e.g. mutations e.g. CAT > GC. Some callers represent this as C>G, A>C, and T>_. Others might represent it as CAT > CG. Multiple issues can arise. In PCAWG, overlapping indel/SBS calls from different callers were included in the indel VCFs.
SBS.vcf	This argument defaults to NULL and is not used. Ideally this should be an in-memory SBS VCF as a data frame. The rational is that for some data, complex indels might be represented as an indel with adjoining SBSs.
sample.id	Usually the sample id, but defaults to "count".

Value

A list of a 1-column ID matrix containing the mutation catalog information and the annotated VCF with ID categories information added. If some ID variants were excluded in the analysis, an additional element discarded.variants will appear in the return list.

ICAMS documentation built on June 22, 2024, 6:47 p.m.