Shulou(Shulou.com)06/01 Report--

Editor to share with you what minfi is, I believe that most people do not know much about it, so share this article for your reference, I hope you will learn a lot after reading this article, let's go to understand it!

Minfi is an R packet for analyzing DNA methylation chips. The official website is as follows:

Http://www.bioconductor.org/packages/release/bioc/html/minfi.html

If we want to use this package for analysis, we first need to read our chip data in R, which is often called import data. For minfi, its design idea is to read the SampleSheet.csv file, find the original data of all samples in the agreed directory structure, and automatically read the information of all samples.

On illumina's official website, we can find templates and test data sets for the corresponding SampleSheet files.

850K:

Https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html

450K:

Https://support.illumina.com/array/array_kits/infinium_humanmethylation450_beadchip_kit/downloads.html

An example of a SampleSheet.csv template for a 450K chip is as follows:

In the SampelSheet file, the first few lines are comment information, the basic information of the sample below [Data].

There can be up to 12 samples on a methylation chip, and each sample is marked according to Sentrix_Position. When the number of samples is more than 12, another chip is needed. For each chip, use Sentrix_ID identification. Minfi uses the Sentrix_ID and Sentrix_Position fields to find the original data of the sample.

For each sample, there will be two .idat files, based on the sample SampleSheet.csv file, with the corresponding file name

200514040030_R01C01_Grn.idat200514040030_R02C01_Red.idat

We just need to organize it into the directory structure shown below.

SampleSheet.csvSentrix_ID/ ├── Sentrix_ID_Sentrix_Position.Grn.idat └── Sentrix_ID_Sentrix_Position.Red.idat

The SampleSheet.csv file is in the first layer, and then the Sentrix_ID corresponding to each chip is a directory. Under each Sentrix_ID directory, is the original data of the sample on the chip. The file name is Sentrix_ID_Sentrix_Position.Grn.idat.

Minfi reads data

After sorting out the SampleSheet.csv file and the corresponding directory structure, you can read it in R.

The read.metharray.sheet function reads the SampleSheet.csv file, the first parameter is the directory where the file is located, and the second parameter is the name of the file, which supports regular expressions. If you are not used to regularities, just specify the corresponding file name directly.

Read in the sample sheet for the experiment

Targets

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.