| title | author | date | output |
|---|---|---|---|
Cell Composition |
Quynh Nhu Nguyen |
March 4th 2023 |
html_document |
To examine the importance of accounting for cellular composition in DNA methylation analysis, we are going to download a GEO dataset used in an analysis of whole blood data.
The minfi package has a function to read data directly from GEO. Run the following commands. Note that this command downloads 64.7 MB of data and can take several minutes, depending on your download speed.
library(minfi)
grset=getGenomicRatioSetFromGEO("GSE32148")
This creates an object of class:
class(grset)
which is quite convenient. Use the function pData to examine the sample information table and determine which column includes the age of the individual.
What is the name of this column?
names(pData(grset))
pData(grset)[1,]
## note age is here
pData(grset)[1,"characteristics_ch1.1"]