How to know whether identified mutation signatures from my data are listed in COSMIC site?
I used SomaticSignatures package in R and got some mutation signatures.
I usually designated specific signatures by comparing my signatures and listed signatures in COSMIC site through my eye. https://cancer.sanger.ac.uk/cosmic/signatures_v2
I would like to know whether there are more statistically reasonable method to match the most similar signature to each of my signature.
1 answer
There are packages available specifically for that purpose, such as MutationalPatterns or deconstructSigs.
Log in to answer this question.
More posts like this
-
Searching for a specific somatic mutation in Illumina data
written by manfi •
-
fitting a copy number profile to know CNV signatures
written by Bogdan
-
Drilling down to the right samples in COSMIC
written by LauferVA
-
Which clustering method is preferable to use in Heatmap?
written by elefth.pavlos •
-
mutational signatures in different tumor samples
written by lzy •
-
Software to analyse mutational signatures other than DeconstructSigs R package
written by peterodonovan •
-
Any idea about validating bedtools shuffle did what I desired?
written by morovatunc
-
Displaying somatic mutational signatures
written by kezcleal
-
Cosmic mutation signature
written by agicict
-
What is a microarray "signature" and how can I compare my sample to a known signature?
written by JacobS
You should be able to download a VCF (or similar file) from COSMIC and use that to automate your lookup operation.
Thank you for your comment. Do you mean that I should identify mutation signature from the VCF files and then compare it with my data?
What do you mean by signatures? I'm just saying that you should be able to automate what you're doing manually using either downloadable files or querying APIs or a combination of both.