ICAMS: AddAndCheckSBSClassInVCF – R documentation

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AddAndCheckSBSClassInVCF

Add and check SBS class in an annotated VCF with the corresponding SBS mutation matrix

Add and check SBS class in an annotated VCF with the corresponding SBS mutation matrix

AddAndCheckSBSClassInVCF(vcf, mat96, mat1536, mat192 = NULL, sample.id)

`vcf`	An in-memory VCF file annotated with sequence context and transcript information by function `AnnotateSBSVCF`. It must not contain indels and must not contain DBS (double base substitutions), or triplet base substitutions etc., even if encoded as neighboring SBS.
`mat96`	The SBS96 mutation count matrix.
`mat1536`	The SBS1536 mutation count matrix.
`mat192`	The SBS192 mutation count matrix.
`sample.id`	Usually the sample id, but defaults to "count".

The original vcf with three additional columns SBS96.class, SBS192.class and SBS1536.class added.

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