R Methy III: Read Data

Read the files into R

Use the functions in minfi for reading the idat files into R.

I suggest you start by storing the path to the data folder in a variable called dataDir.

Now we will read the sample sheet and the IDAT files from the directory containing the data.

• Read your sample sheet using the function read.metharray.sheet(),
• then read in the IDAT files using the function read.metharray.exp()

Take a look at the object containing the methylation data.

Questions:

Study the output properties of your objects and answer the following questions:

1. Which methylation array do these files come from?
2. What type of R object do you have?
3. How many samples and how many markers (features) are available in the data?

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