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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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normalize XP-nSL #51

Closed Huyuxi08 closed 3 years ago

Huyuxi08 commented 3 years ago

Hi,

I'm currently trying to perform your new method XP-nSL on my data. I have normalized the results with non-overlapping windows of 20kb, and the command I used is norm --xpnsl --files hm_eas_cen_chr1.xpnsl.out --bp-win --min-snps 20 --winsize 20000. However I'm not sure what the results from column 4 to column 7 in the *.windows file represent. The manual describes it like this:

For XP stats:

<# scores in win> I am a bit confused about the meaning of "gt" and "lt". Does the former one mean the positive scores, and the latter one mean negative scores? The *.windows file I got is as follows: 1 20001 273 0.014652 0 100 5 2.15695 0.360257 20001 40001 259 0.169884 0 100 5 2.90022 0.62959 40001 60001 250 0.868 0 5 5 4.83393 1.36376 60001 80001 239 1 0 1 100 3.38311 2.06651 80001 100001 235 0.595745 0 5 100 3.63697 0.842613 Thanks in advance!
szpiech commented 3 years ago

Hi there, sorry for the confusion. "gt" == "greater than" and "lt" == "less than", and you are correct these essentially correspond to extreme positive and extreme negative score stats.