Question: Determining the subjects to use after obtaining a PC plot of population substructure
gravatar for Sheila
24 months ago by
United States
Sheila300 wrote:

I am doing QC for a GWAS analysis. I used pc-AIR and pc relate (two Bioconductor Packages) to determine the relatedness and population substructure of my given dataset. I compared it to 1000 genomes data and have a plot comparing the first two PCs in my PCA analysis. In general, what is the best practice for excluding subjects from a study after visually scrutinizing the PC plot. Is there a specific method (ie R package) to use that's considered best practice? or do I arbitrarily decide that base on the graph I want to include a certain set of subjects?

Thanks for your thoughts, in advance.

ADD COMMENTlink written 24 months ago by Sheila300

Here you will find a very detailed answer. Also, I suggest you give a look to GENABEL manual ( In paragraph 5.3 they describe the method used for outlier detection.

ADD REPLYlink written 24 months ago by Fabio Marroni2.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1725 users visited in the last hour