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This article shows you how to use plink for linkage imbalance analysis, the content is concise and easy to understand, can definitely brighten your eyes, through the detailed introduction of this article, I hope you can get something.

Plink is one of the common tools for linkage disequilibrium analysis, which requires two basic input files with suffixes of ped and map. The ped file format has been described in detail in previous articles, and only the map file is introduced here.

The map file mainly stores the name and location information of SNP sites, which are as follows

1 snp1 0 11 snp2 0 2

There are four columns, each row represents a SNP locus, the first column represents the name of the chromosome on which the SNP locus is located, the second column represents the ID of the SNP locus, usually the rs number, or the custom ID; third column represents the genetic distance of the SNP locus, which can be filled with 0 if there is no actual value, and the fourth column represents the position of the SNP locus on the chromosome.

There are two ways for plink to perform LD analysis:

1. Analyze two specified SNP sites

The command is as follows

Plink-file test-ld snp1 snp2

In the log information, the results of the LD analysis are output

LD information for SNP pair [snp1 snp2] R-sq = 0.009 D' = 0.163 Haplotype Frequency Expectation under LE-AG 0.116 0.139 CG 0.300 0.278 AT 0.217 0.194 CT 0.366 0.389 In phase alleles are AT/CGAnalysis finished: Sat Jun 23 11:48:35 2018

The values of R2 and D' are given, and the frequencies of different haplotypes are also given.

two。 All SNP loci were analyzed.

The command is as follows:

Plink-file test-rplink-file test-R2

-- r outputs the results of all LD analyses directly, while-R2 filters the results based on R2 values. In the actual analysis, the number of SNP sites is very large, if not filtered, the result file will be very large. The filter parameters are as follows

-- ld-window

The default value is 10, which limits a SNP locus to a maximum of 10 other SNP loci for LD analysis.

-- ld-window-kb

The default value is 1Mb, and only SNP sites within the distance of 1Mb are analyzed.

-- ld-window-r2

This parameter can only be used with the-- R2 parameter, with a default value of 0.2. the output is filtered and only LD analysis results with R2 greater than the parameter value are output.

The output file is plink.ld. This file shows the R or R2 values between SNP sites. Examples are as follows

CHR_A BP_A SNP_A CHR_B BP_B SNP_B R 1 1 snp1 1 2 snp2-0.108465

By specifying the-- ld-snp parameter, you can also analyze only the linkage relationship between one SNP locus and other loci, as follows

Plink-file test-R2-ld-snp snp1-ld-window-kb 1000-ld-window 99999-ld-window-r2 0

The above two methods have more advantages and disadvantages, the first method will give two values of D' and R2, the second method will only give R value, the first method can only analyze the linkage relationship between two SNP sites at a time, and the second method can analyze the linkage relationship between multiple SNP sites at a time.

The above content is how to use plink for linkage disequilibrium analysis. Have you learned any knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.

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