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!
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.
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: