Scripts and lists of CpGs which are seen as non-variable in GEO data on the 450K.
https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-017-0320-z
library(RCurl)
x <- getURL("https://raw.githubusercontent.com/redgar598/Tissue_Invariable_450K_CpGs/master/Invariant_Buccal_CpGs.csv")
y <- read.csv(text = x)
nonvariable_buccal<-y$CpG
In a study of 25 blood samples @lmcewen ~108,000/114,000 blood invariable CpGs were non-variable.
In PAWS @redgar598 (buccals) 99.5% of the buccal non-variable CpGs are also invariable in PAWS
In Lisa's training data (1032 buccals) the overlap was 98,850 out of 120,009 (82%).
In a study of 75 blood samples the overlap was 101,864 out of 102,230 (the number left after other filtering) (99.6%)