Error when changing the database for minfi dropLociWithSnps

Question

[Ellen O]

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

Answer 1

[steffanchristiansen]

Did you ever find a solution to the issue? I have the same issue with the getSnpInfo() function in minfi version 1.30.0.

Best, Steffan

Answer 2

[Satu]

Has anyone solved this? I am struggling with the same thing and haven't found any information how to actually use it.