Question: Chromosome arm loss and --maxhomozygousloss default
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gravatar for twtoal
11 months ago by
twtoal0
twtoal0 wrote:

I see that the default value for the PureCN.R --maxhomozygousloss option is 0.05,1e+07.  Does this mean that if entire chromosome arms are lost, they must not total more than 5% of the genome?  

 

purecn maxhomozygousloss • 230 views
ADD COMMENTlink written 11 months ago by twtoal0
Answer: C: Chromosome arm loss and --maxhomozygousloss default
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gravatar for markus.riester
11 months ago by
markus.riester110 wrote:

It means that homozygous losses are not accepted in the optimization when the corresponding segment is larger than 10Mb or when more than 5% of a chromosome (whole chromosome, not arm) is completely lost. This is mainly to avoid wrong solutions where a complete chromosome is assigned to a homozygous loss state.

The default is calibrated for medium sized panels. With small panels, MTAP/CDKN2A deletions might exceed this cutoff if you have only few other genes surrounding them and you might want to increase. Future versions might be a bit smarter here, see https://github.com/lima1/PureCN/issues/50.

 

ADD COMMENTlink modified 11 months ago • written 11 months ago by markus.riester110
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