Converting VCF to VRanges
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arsala521 ▴ 10
@arsala521-10976
Last seen 5.8 years ago

Hello

I want to use SomaticSignatures package in my study. It is mentioned in the documentation of the package that the starting point of analysis is the VRanges object. I have variants in the VCF file format. I am using the code that is used to convert VCF to VRanges but I am facing some problem.

I have four VCF files of four different cancer types. I want to construct a single VRanges object from these four files such that in VRanges object, with every variant, cancer type is present in the study column of VRanges.

Would someone please help me with this?

Regards

somaticsignatures vranges • 1.2k views
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Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 3.0 years ago

You can concatenate different VRanges to one, e.g.:

vr = c(vr1, vr2, vr3)

To add new metadata to a VRanges, such as cancer type, use:

mcols(vr)$var = "your value"

Please also have a look at the extensive documentation of the VariantAnnotation package.

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Thank you so much.

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I think you mean

mcols(vr)$cancer.type = "your value"
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Thank you, Michael! I have corrected this in my answer.

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