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Question: Sequence Context of Somatic Variants
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gravatar for arsala521
16 months ago by
arsala52110
arsala52110 wrote:

Hello

I am using SomaticSignatures package. When we extract sequence context of single nucleotide variants using the command like this

sca_motifs = mutationContext(sca_vr, BSgenome.Hsapiens.1000genomes.hs37d5)

we get two additional columns in vranges, alteration and context.

If ref is G and alt is A, then CT is mentioned in alteration column, which is according to the opposite strand. I want to ask whether in this case neighboring nucleotides provided in context column is also according to the opposite strand.

Would someone please answer my question?

 

ADD COMMENTlink modified 16 months ago by Julian Gehring1.3k • written 16 months ago by arsala52110
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gravatar for Julian Gehring
16 months ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:

If the alteration is transformed to a pyrimidine reference (T or C), the mutation context is also transformed accordingly by default. You can check this by disabling the transformation in the mutationContext function, by setting unify = FALSE

ADD COMMENTlink written 16 months ago by Julian Gehring1.3k

Hi, I am also using your SomaticSignatures, but I cannot transfer your example GRange data to VRange format.Posted question is at makeVRangesFromGRanges throws coercing "factor" to "NA" error can you help me to solve this problem? Thanks

ADD REPLYlink written 16 months ago by solo777310

Thank you so much

 

ADD REPLYlink written 16 months ago by arsala52110
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