A tutorial on how to do genomewide association studies gwas in plink. For the sake of reproducibility, one could use plink directly from r. R is flexible in types of data without the need to merge them. Recode and reorder a sample a basic, but often useful feature, is to output a dataset.
Plink uses the rserve package to communicate with r. In order to perform analyses of largescale genomic data in r, we developed two r packages, bigstatsr and bigsnpr, that provide a widerange of building blocks which are parts of standard analyses. If there are missing genotypes, these will by default be assigned as na. The steps described involve the identification and removal of dna samples and markers that introduce bias to the study. Dos window or unix terminal followed by a number of options all starting with option to specify the data files methods to be used. A software to analyse phenotypegenotype data it is run from the command line why should we use plink. The plink executable file should be placed in either the current working directory or somewhere in the command path. Rplinkseq is an r package that allows access to plinkseq projects directly. Plink currently supports following functionalities. A phenotype has been simulated based on the genotype at one snp.
Management of bgen file is based on bgen lib written by. It has provided many sample datasets which help with learning to use. The software is designed flexibly to perform a wide range of basic, largescale genetic analyses. Genotyping arrays enable the direct measurement of an individuals genotype at thousands of. The r package plink has been developed to facilitate the linking of mixedformat tests. Both these commands will create two new files plink. This protocol details the data quality assessment and control steps that are typically carried out during casecontrol association studies. Output files are valid input for extractexclude in a future plink. Read a plink binary data file as a snpmatrix the package plink saves genomewide association data in groups of three files, with the extensions.
Efficient analysis of largescale genomewide data with. The library can be accessed via the pseq command line tool, or through an r interface. Item response theory based methods are used to compute linking constants and conduct chain linking of unidimensional or multidimensional tests for. How to get and interactive session through uge for further information, load plink into your environment, and invoke plink. Principal component analysis pca 101, using r towards. The scripts are based on plink, prsice, and r, which are commonly used, freely available software. How to run plink interactively to run plink interactively on the cluster please request an interactive node with qrsh see. Plinkseq for analyzing largescale genome sequencing data. Would you suggest any other option in plink r any other software. Statistical analysis of genomewide association gwas data.
I want to write a batch script which forwards a local port on my machine to the server, dataexchange. They are currently based on correlations between genotype allele counts. Ibd can be estimated using genomewide ibs data using software such as plink. I did some testing and it is possible to convert these back to plink, but you are still missing key information. Statistical analysis of genomewide association gwas data jim stankovich menzies research institute. In this tutorial, we will walk through using plink to work with the data, using a range of features. This is a brief list of all file extensions generated by plink 1.
Yes, plink expects two columns for each snp genotype, and, if numbers are provided as genotypes in the pedraw file, it will assume that these are in the 1234 format for acgt. In large datasets, it is typical for the plink data to be organized by. Plink is an opensource whole genome association analysis toolset, designed to. This introduction to the r package plink is a slightly modi ed version ofweeks 2010, published in the journal of statistical software. This tutorial is a combination of miniguide to plink and practical exercise. The corresponding phenotypic data and plink analysis results can be added as they are generated, enabling immediate incorporation of these latest data into analyses. Creates a manhattan plot from plink assoc output or any data frame with chromosome, position, and pvalue. Dos window or unix terminal followed by a number of options all starting with option to specify the data. R has its own and more powerful language and its procedures are open to modify. The code relies partially on those written in plink by christopher chang. These functions compute response probabilities for speci. I performed a gwas in plink and now i would like to look at the data for a small set of snps listed one for each line, in a file called snps. I would like to create a ld vs distancecm plot in r using an output from plink. Rplinkseq is implemented as an extension library, which enables access to the plink seq.
R has a flexible and highquality graphical facility. The plot at the very beginning af the article is a great example of how one would plot multidimensional data by using pca, we actually capture 63. Plink is a free, opensource whole genome association analysis toolset, designed to perform a range of basic, largescale analyses in a computationally efficient manner. Dear all i have a genotype data for snp in cattle, i calculated r 2 by plink. Optionally, information about snps can be read from a. All commands involve typing plink at the command prompt e. How can i do linkage disequilibrium ld test for a list. For this, i have to do association for all possible combinations of one snp one variable. Plink is a command line program clicking on an icon with the mouse will get you nowhere. Plink is a free, commonly used, opensource wholegenome association analysis toolset designed by shaun purcell. Introduction to the plink software plink overview i summary statistics for quality control i allele, genotypes frequencies, hwe tests i missing genotype rates i inbreeding, ibs and ibd statistics for individuals and pairs of individuals i nonmendelian transmission in family data. Item response theory based methods are used to compute linking constants and conduct chain linking of unidimensional or multidimensional tests for multiple groups under a common item design.
Introduction to plink tutorial aimsh3a bionet april 2015 1 set up 1. This means that all the core features of the plink. The focus of plink is purely on analysis of genotypephenotype data, so there is no support for steps prior to this e. How can i do linkage disequilibrium ld test for a list of snp. Plink is a very efficient commandline software very useful for preprocessing of genomewide data chang et al.
The package plink saves genomewide association data in groups of three files, with the extensions. Rplinkseq is an r package that allows access to plink seq projects directly from r, so that r s rich set of statistical and visualisation tools can be utilised. All results are written to files with various extensions. Plinks primary job is management and analysis of positionbased snplike data. There is no population data available and the only thing i want to do is, which tagsnps are in ld with each snps. I have been trying with different ldwindowkb numbers but i can not plot them in r. Whilst not official r packages one software suite in particular is worthy of mention. Plink reads a data file exported by the plink software with extension. Plink provides a simple interface for recoding, reordering, merging, flipping dnastrand and extracting subsets of data. Plink needs a structured data ped and map file or binary version of those. Contribute to tshmaklassosum development by creating an account on github. The simulated data and scripts that will be illustrated in the current tutorial provide hands.
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