CreateOneColID115Matrix: Create one column of the matrix for an indel catalog from...
In steverozen/ICAMSxtra: ICAMSxtra
Description
Usage
Arguments
Value
Description
Create one column of the matrix for an indel catalog from one in-memory VCF.
Usage
1
CreateOneColID115Matrix(ID.vcf, SBS.vcf = NULL)
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.
Value
A list of a 1-column matrix containing the mutation catalog
information and the annotated VCF with ID categories information added.
steverozen/ICAMSxtra documentation built on Feb. 9, 2022, 7:01 a.m.
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Description Usage Arguments Value
Description
Create one column of the matrix for an indel catalog from one in-memory VCF.
Usage
1 | CreateOneColID115Matrix(ID.vcf, SBS.vcf = NULL)
|
Arguments
ID.vcf |
An in-memory VCF as a data.frame annotated by the
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 |
Value
A list of a 1-column matrix containing the mutation catalog information and the annotated VCF with ID categories information added.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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