custom panel normalization

[idanbudin]

Hi,
I am using whichSignatures on variants that I've found on specific genome regions (about 1 gb total).
I'm using mut.to.sigs.input to create the input data frame and using signatures.cosmic as the ref.

My question is about how should I normalize the input.

I've already derived the trinucleotide counts table (assigned it to tri.counts.targeted) using trinucleotideFrequency on a hg19 fasta intersected with my BED file.

I've thought about two options:

1. using tri.counts.method = tri.counts.genome/tri.counts.targeted
2. instead of using the absolute counts of the tables above, using normalized tables in order to normalize my data by the ratio of each trinucleotide count fraction in my panel regions compared to the i.e:
   tri.counts.targeted.norm <- tri.counts.targeted/sum(tri.counts.targeted)
   tri.counts.genome.norm <- tri.counts.genome/sum(tri.counts.genome)
   and then using: tri.counts.method = tri.counts.genome.norm/tri.counts.targeted.norm

any advice regarding that issue will be appreciated!
greetings,
Idan

[shenhaizhongdechanrao]

Dear idanbudin:
Hi, I am also trying this thing. Can you give me some suggestions?