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szpiech / selscan

Haplotype based scans for selection
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norm xpehh output format #57

Closed YuanwenGuo closed 3 years ago

YuanwenGuo commented 3 years ago

Hello,

I am trying to get normalized xpehh values within windows using commands: norm --xpehh --files $input --bp-win --winsize 20000

The output has 9 columns, could you please provide header information for each column? Which one is the normalized xpehh? The output is as follows: 1 20001 105 0 0 1 100 0.427604 -1.47963 20001 40001 355 0 0.0478873 100 1 0.726029 -2.30077 40001 60001 949 0 0 1 100 1.21741 -1.75812 60001 80001 532 0 0 100 100 1.76434 -1.32259 80001 100001 667 0 0 100 100 1.85594 -0.384881 100001 120001 488 0 0 100 100 1.85094 -1.61615 120001 140001 529 0.0415879 0.00378072 100 100 2.14336 -2.10125 140001 160001 404 0 0 100 100 0.782917 -1.62801 160001 180001 571 0 0 100 100 1.74265 -1.46968 180001 200001 598 0 0 100 100 1.70662 -0.920458

Thank you, Yuanwen

YuanwenGuo commented 3 years ago

Sorry I just realized there are descriptions about xpehh norm results in the manual pdf. It looks like I can find max, min and etc in the table, but is there a normalized value for the window which could be used for plotting?

Thank you for the help, Yuanwen

szpiech commented 3 years ago

Hi there, I think your best option for a single value per window is to plot the max or min, depending on which target population you're interested in.

YuanwenGuo commented 3 years ago

Thank you for the suggestion!

Best, Yuanwen