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This article introduces the R language processing gene chip sequencing SNP data analysis is how, the content is very detailed, interested friends can refer to, hope to be helpful to you.

The final data format is as follows: image.png, the first column is the probe id, the second column is the chromosome number, the third column is the chromosome location, the fourth column is the genotype of the first sample, and then the genotype of each sample.

It is equivalent to that each row is a site and each column is a sample.

This dataset is downloaded from the link https://popgen.nescent.org/StartSNP.html

Image.png

The main inner tube of today's tweet is also referenced from this link. The dataset of this link is more than 500 samples and more than 3000 sites. I only selected 30 samples and 996 sites.

The first step is to read in the data

Because it is stored in csv format, read it directly using the read.csv () function

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