Raw DNA methylation data for Sabedot et al.

Published: 06-02-2020| Version 3 | DOI: 10.17632/cgrz6zztfg.3
Contributors:
Thais Sabedot,
Houtan Noushmehr

Description

Raw DNA methylation data (Illumina EPIC array) for Sabedot et al.

Files

Steps to reproduce

### R code to read in IDAT files and generate beta-values library(minfi) idat <- read.metharray.exp(targets = NULL,base=getwd(),recursive = TRUE) proc <- preprocessNoob(idat, offset = 0, dyeCorr = TRUE, verbose = TRUE, dyeMethod="reference") detP <- detectionP(idat, type = "m+u") proc.r <- ratioConvert(proc) is.na(assays(proc.r)$Beta) <- (detP[rownames(proc.r), colnames(proc.r)] > 1E-16) beta <- assays(proc.r)$Beta