Hi,

Where do the MAFs come from in minfi? We are using the dropLociWithSnps to remove probes with common snps and would like to know which population the internal MAFs used by minfi are from.

Thanks. 

wz

The default annotation object (which is all we are providing at the moment) contains the UCSC Common SNP tables for dbSnp 132, 135 and 137.  If you read the documentation on MAF for those tables on UCSC you'll see that it is basically impossible to track down the answer to this (great) question: all UCSC requires is that the SNP has some MAF reported in some population. I believe that if multiple MAFs are reported (for different populations) the highest MAF is used. Also note that known SNPs without MAF information in dbSNP is not part of these tables.