Error when changing the database for minfi dropLociWithSnps

Error when changing the database for minfi dropLociWithSnps

2

I am currently filtering Illumina MethylationEPIC data with minfi, which has run smoothly so far. To remove polymorphic CpGs and SBEs I use the following code:

NormFlt <- dropLociWithSnps(NormFlt, snps=c("SBE","CpG"), snpAnno="SNPs.147CommonSingle")

And get the following error:

Error in getSnpInfo(object, snpAnno = snpAnno) :
snpAnno '147CommonSingle' is not part of the annotation

I get the same error no matter what SNP database I provide, but it runs fine when I do not specify a database. I’m trying to figure out what the problem is but no luck so far. I’m also struggling to find doc on what database it uses by default? I figured since 147 is the most recent it would be the best one to use. Am I using snpAnno incorrectly?

Any help would be greatly appreciated! Thanks.

R version 3.4.0 Patched, minfi_1.22.1


SNP


minfi


methylationEPIC


illumina


methylation

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