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xihaoli / STAARpipeline

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline
GNU General Public License v3.0
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Regarding the cMAC value #23

Open ryshi06 opened 1 week ago

ryshi06 commented 1 week ago

Hello Dr. Li,

Thanks again for this great package. I have a quick question that why some cMAC output has decimal points. Based on my understanding, this might be caused by the genotype imputation, but I cannot find any related scripts illustrating this. Can you please help me clarify this. Thank you!

Best, Ruyu

xihaoli commented 1 week ago

Hi Ruyu,

Thanks for reaching out. Yes, if after your variant QC steps, there are still variants with missing genotypes in your dataset, STAARpipeline will then impute either by mean dosage (default) or the minor allele across all samples (see here for an example). Thus, if you are using "mean" imputation, your cMAC may not be an integer.

Best, Xihao