Sequence Context of Somatic Variants
1
0
Entering edit mode
arsala521 ▴ 10
@arsala521-10976
Last seen 7.7 years ago

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?

 

somaticsignatures mutation context • 1.2k views
ADD COMMENT
0
Entering edit mode
Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 4.9 years ago

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

Thank you so much

 

ADD REPLY

Login before adding your answer.

Traffic: 544 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6