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MAF snps_removed is wrong #36

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sheshen22 opened this issue Dec 12, 2023 · 2 comments
Open

MAF snps_removed is wrong #36

sheshen22 opened this issue Dec 12, 2023 · 2 comments
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@AliSajid

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@sheshen22
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Thank you to the developer for creating this software.
When the MAF is set, it can accurately delete SNPs. While this does not affect the outcomes in the main file, the snps_removed file that is generated is incorrect.
Using plinkCoxSurv, Figure 1 shows 3 SNPs as an example, and Figures 2 and 3 are for MAF 0.4. It is evident that the snps_removed file is incorrect.
The same happens when I analyze using my own files.
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@aarizvi
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aarizvi commented Dec 20, 2023

Indeed, this is a bug. I'm not actively maintaining this right now do plan on fixing this.

@AliSajid if you have any time could you take a peak at this?

@AliSajid
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@aarizvi I'll take a crack at it. Self-assigning.

@AliSajid AliSajid self-assigned this Dec 20, 2023
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@AliSajid AliSajid

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@AliSajid @aarizvi @sheshen22