Create one column of the matrix for an indel catalog from *one* in-memory VCF.
CreateOneColIDMatrix(
ID.vcf,
SBS.vcf = NULL,
sample.id = "count",
return.annotated.vcf = FALSE
)
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.
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.
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.
Usually the sample id, but defaults to "count".