inst/scripts/make-data.R

In immunomethylomics/FlowSorted.BloodExtended.EPIC: Illumina EPIC data on extended immunomagnetic sorted blood populations

### =========================================================================
### FlowSorted.BloodExtended.EPIC RGChannelSet
### -------------------------------------------------------------------------
##Local processing
setwd("I:\Dropbox (Christensen Lab)\Extended library\Raw_Data\Raw_Data")
library(minfi)

sheet<-read.metharray.sheet(getwd())
FlowSorted.BloodExtended.EPIC <- read.metharray.exp(targets = sheet,
                                                    extended = FALSE)
save(FlowSorted.BloodExtended.EPIC,
    file = "FlowSorted.BloodExtended.EPIC.RData",
    version = 3, compress = "xz")
## Files are available as GSE167998
library(minfi)
library(GEOquery)
getGEOSuppFiles("GSE167998")
untar("GSE167998/GSE167998_RAW.tar", exdir = "GSE167998/idat")
idatFiles <- list.files("GSE167998/idat", pattern = "idat.gz$", full = TRUE)
sapply(idatFiles, gunzip, overwrite = TRUE)
FlowSorted.BloodExtended.EPIC <- read.metharray.exp("GSE167998/idat")
geoMat <- getGEO("GSE167998")
pD <- pData(geoMat[[1]])
sampleNames(FlowSorted.BloodExtended.EPIC) <- sub(".*_5", "5",
                                                sampleNames(FlowSorted.BloodExtended.EPIC))
rownames(pD) <- pD$title
pD <- pD[sampleNames(FlowSorted.BloodExtended.EPIC),]
pData(FlowSorted.BloodExtended.EPIC) <- pD
FlowSorted.BloodExtended.EPIC
save(FlowSorted.BloodExtended.EPIC,
    file = "FlowSorted.BloodExtended.EPIC.RData", version = 3, compress = "xz")