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suchestoncampbelllab / gwasurvivr

GWAS Survival Package in R
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MAF snps_removed is wrong #36

Open sheshen22 opened 9 months ago

sheshen22 commented 9 months ago

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. image image image

aarizvi commented 8 months ago

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 commented 8 months ago

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