Dear Bioconductor Community,
I want to understand the function "dropLociWithSnps" within minfi
GRset <- dropLociWithSnps(GRset, snps=c("SBE","CpG"), maf=0)
minfi developers said
Probe, CpG and SBE correspond the SNPs present inside the probe body, at the CpG interrogation and at the single nucleotide extension respectively. We strongly recommend to drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension.
Does anyone know the meaning of CpG interrogation and single nucleotide extension(SBE)?
There is no explanation about them.
I think these words are key words which help me to understand why I need to drop the probes that contain either a SNP at the CpG interrogation or SBE.
Thank you in advance.