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hardingnj / xpclr

Code to compute the XP-CLR statistic to infer natural selection
MIT License
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How to set the parameters #103

Open zishanw opened 6 months ago

zishanw commented 6 months ago

Hi, @hardingnj

Thank you for writing this implementation.

I was using it to detect the genomic regions of various crops under artificial selection, and would like to know what should I consider when setting the parameters, especially these four below when using vcf as input:

--ld 
--maxsnps
--size
--step

And when I ran the program I got the output log file as below:

log

Do you have any ideas about it? Or can I just ignore it since I can get a result file despite the error.

Thank you for your time and support.

zishanw commented 6 months ago

Hi, @hardingnj

Another problem is that more than 80% of the xpclr values of the output files are negative. Is this normal?

Thank you for your help!

hardingnj commented 6 months ago

Hi, I don't think I would really recommend XPCLR as a method for detecting selection in artificial selection. It's really designed for wild populations with some maintained level of variation. You may break some of the method's assumptions.

If it were me, i'd look at some measure of divergence or local diversity.