exomeCopy copy number setting
1
0
Entering edit mode
@cafelumiere12-7513
Last seen 3.5 years ago
United States

Hello,

I have been using exomeCopy with no problem; however I was wondering if anyone has any insight about setting the possible copy number while running the exomeCopy function to get CNVs? I have trid both S=1:4 or 1:6 but I'm not sure if there is a general rule for this. Can I set 1:4 only? Do I need to use 1:6? Or is 1:10 even?

Basically it's the S setting in the following sample code:

fit <- exomeCopy(example.counts["chr1"], sample.name = exome.samples[3], X.names = c("log.bg", "GC", "GC.sq", "width"), S = 0:6, + d = 2)

Any suggestion is appreciated. Thanks!

cnv exomecopy • 738 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 hour ago
United States

I would recommend staying within 0:6 (where 2 is normal diploid, so allowing for triplication). Or if you need to go higher, because you suspect there are more than triplication in the samples, I'd recommend you switch to something like ExomeCNV, which allows arbitrary values in its use of the DNAcopy CBS algorithm.

ADD COMMENT

Login before adding your answer.

Traffic: 308 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