Many people find that it easiest to learn by example. On the medical bundle tab in the analyses group, click meta analysis and meta regression to display the meta analysis and meta regression dialog. This website includes a download page, brief documentation in our wiki and a registration page. If you use metal please fill out a copy of the registration form or email goncalo abecasis.
Which is the best tool for metaanalysis of gwas data. Lets use metal to run a fixedeffect metaanalysis weighted by sample number fore each study. Metal, including source code, documentation, examples, and. This archive includes a small example of how metal can be used to meta analyze study results. Now i have genotyped one snp in this sample and calculated the p value for the allelic. Metaanalysis is a research process used to systematically synthesise or merge the findings of single, independent studies, using statistical methods to calculate an overall or absolute effect.
To enable correction for sample overlap in your sample size weighted metaanalysis, use. Metaanalysis software forest plot radial plot ncss. In this practical we will run a gwa metaanalysis using metal. Fictitious example do individuals who wear sunscreen have fewer cases of melanoma than those who do not wear sunscreen.
We, and others, have used metal for performing metaanalysis of gwas to identify loci. It has been around for more than 10 years and has been used in hundreds of analyses and publications. Metaanalysis method there are three different metaanalysis methods available controlled by the method optionmethod 1. Meta analysis is a statistical technique for combining the findings from independent studies. The glucose data this example examines evidence for association between fasting glucose levels and genetic markers in the g6pc2 chr. I am performing a metaanalysis of multiple gwas data and now, after an intensive qc, i have to choose a suitable software for doing it. Brief overview of methods and general hints description r package meta is a userfriendly general package providing standard methods for meta analysis.
The support staff are always helpful and respond quickly when questions arise. The cran meta analysis task view is exceptionally wellorganized listing r. In a few guided examples, we are loading some data, calculating effect sizes and conducting a meta analysis of a fictional data set. Second edition evidencebased medicine supported by sanofi. It extends excel with several functions for input and output of meta analysis data, and a menu that offers access to output both in table and graphical format, options, examples, and this user guide, among other things. Jul 17, 2014 however, r is the natural platform for meta analysis both because of the myriad possibilities for statistical analyses that are not generally available through the specialized software, and because of the many packages devoted to various aspects of meta analysis. If available studies are too few or too different a metaanalysis may not be appropriate. Metal can combine either a test statistics and standard errors or b pvalues across studies taking sample size and direction of effect into account. This tutorial walks you through the basic concepts. The following is an example of a meta analysis conducted in the medical bundle.
The metafor package implements various meta analytic models, methods, and techniques that have been described in the literature. By default, metal combined pvalues across studies sample size, direction of effect. May, 2016 the most reliable source of evidence based medicine. A basic tutorial arindam basu university of canterbury may 12, 2017 concepts of metaanalyses meta analysis refers to a process of integration of the results of many studies to arrive at evidence syn. The meta analysis procedures in ncss are easytouse and validated for accuracy. The metaanalysis function of jasp is based on the aforementioned metafor r package. Metal provides a computationally efficient tool for meta analysis of genomewide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. It explains the background to these methodologies, what is involved, and how to get started, keep going, and finish. Meta analysis in excel metaxl is a tool for meta analysis in microsoft excel. I wish to test the potential association between candidate gene polymorphism and specific disease risk in different populations.
Nine steps to meta analyses we recommend in general the following nine steps of meta analysis. Pdf metal provides a computationally efficient tool for metaanalysis of. Oct 09, 2015 while the worked example is the analysis of a correlational dataset, the general meta analytic process described in this paper is applicable for all types of effect sizes. Meta analysis is most often used to assess the clinical effectiveness of healthcare interventions. Ncss includes tools for performing meta analysis of means, proportions, correlated proportions, and hazard ratios. Glass, 1976, p3 metaanalysis techniques are needed because only. Metal analysis is important for environmental protection and public health. These nine steps are in general applicable to all metaanalyses. From literature it seems that the most used tool is. The extracted data depends on the research question, but it may include information such as sample size, patient characteristics, length of study, and a statistical measure, such as confidence interval, odds ratio, risks ratio, mean difference, or hazard ratio. I was able to run a meta analysis in reasonable time. Free downloads comprehensive metaanalysis software.
A meta analysis is a statistical overview of the results from one or more systematic. Students are able to return to our computer lab to complete a meta analysis assignment independently after an initial faculty demonstration session. Contribute to statgenmetal development by creating an account on github. Metaanalysis for linear and nonlinear doseresponse.
Gwa metaanalysis metal practical in this practical we will run a. Jasp is a free, opensource program used to perform statistical analysis tests by using r packages. The gwama genomewide association metaanalysis software has been. The analysis should include published and unpublished results to avoid publication bias. The metal software is designed to facilitate metaanalysis of large datasets such as several whole genome scans in a convenient, rapid and memory efficient. The links below demonstrate how the models, methods, and techniques described in the respective articleschapters can be applied via the metafor package. Metal is a tool for metaanalysis genomewide association scans. Does the meta analysis include any appropriate relevant studies that may have had negative outcomes. In accordance with the principles of integrated analysis, each article was considered as independent, with different ph values, initial heavy metal concentrations, algal source areas, and use of either living or nonliving algae. This article demonstrates the stepbystep process of meta analysis using a recentlypublished study examining the effects of curricular and cocurricular diversity activities on racial bias in college students as an example denson. Meta analysis is a statistical technique, or set of statistical techniques, for summarising the results of several studies into a single estimate. Conceptually, a meta analysis uses a statistical approach to combine the results from multiple studies in an effort to increase power over individual studies, improve estimates of the size of the effect andor to resolve uncertainty when reports disagree. Metaanalysis in medical research pubmed central pmc. While the worked example is the analysis of a correlational dataset, the general metaanalytic process described in this paper is applicable for all types of effect sizes.
I wish to test the potential association between candidate gene polymorphism and specific disease risk in. Metal provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. For example, you can trying issuing the help command, to which metal. The name mix comes from metaanalysis in excel and 2. Complex analyses can be conducted easily using this intuitive software. Provides a computationally efficient tool for metaanalysis of genomewide. Running metaanalysis in r using the metafor package. Metaanalysis of genome wide association studies angus 6. What is a metaanalysis in 1976, glass coined the term metaanalysis metaanalysis refers to the analysis of analyses the statistical analysis of a large collection of analysis results from individual studies for the purpose of integrating the findings. Could anyone suggest a free software for meta analysis. If enabled, metal checks if chromosome and position of a variant match across studies. Software with source files, documentation and example data files are freely. Correction for sample overlap in sample size weighted metaanalysis.
We implemented the meta analysis methodology in an microsoft excel addin which is freely available and incorporates more meta analysis models including the iterative maximum likelihood and profile likelihood than are usually available, while paying particular attention to the userfriendliness of the package. The metal software is designed to facilitate metaanalysis of large datasets such as several whole genome scans in a convenient, rapid and memory efficient manner. The standard approach to trend estimation in meta analysis of exposureresponse relations when only published categoryspecific relative risks and their confidence intervals are available is to fit a weighted linear regression through the origin, in which the dependent variable is the estimated log relative risk, the independent variable is the. So, if reading through our extensive documentation is not for you, you might find it more appealing to walk through a simple metal analysis. Metal is a tool for meta analysis genomewide association scans. Example files this archive includes a small example of how metal can be used to metaanalyze study results. Comprehensive meta analysis cma is essential software for the meta analyst.
Use the links below to jump to the meta analysis topic you would like to examine. Metal analysis is a convenient alternative to a direct analysis of merged data from multiple studies. Other metal analysis needs to be preformed in groundwater, surface water, wastewater, solid waste, soils, and sludge. I was able to run a metaanalysis in reasonable time. Running meta analysis in r using the metafor package. To enable correction for sample overlap in your sample size weighted meta analysis, use. The classical meta analysis compares two treatments while network meta analysis or multiple treatment metaanalysis can provide estimates of treatment efficacy of multiple treatment regimens, even when direct comparisons are unavailable by indirect comparisons 60. An example of a network analysis would be the following. The program allows you to enter the raw measures and already calculated effect sizes. The software facilitates application of complex concepts with real data, helping students see the power of the meta analysis process. This brief tutorial should help you with the first steps in r. An exhaustive search of the literature will require more than r. Since 1980 we have supplied products and services to chemical processing, water treating, and petroleum industries around the world. The chromosome and position fields are propagated to the metaanalysis result file useful when generating manhattan or locuszoom plots.
Toxic metals in drinking water is strictly regulated. In implementing our software for metaanalysis, a primary. Metal meta analysis helper center for statistical genetics. The example is drawn from a recent study of the genetics of glucose levels chen et al, journal of clinical investigation, 2008. Nov 16, 2010 the purpose of this article is to provide higher education researchers with an illustrative example of meta analysis utilizing hierarchical linear modeling hlm. Metal provides a computationally efficient tool for metaanalysis of genomewide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. Meta analysis of trials provides a precise estimate of. Metal provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a.
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