Difference between revisions of "METAL Quick Start"
| Line 1: | Line 1: | ||
| − | == Learning by Example == | + | == Learning by Example == |
| − | Many people find that it easiest to learn by example. So, if reading through our ''extensive'' [[METAL Documentation|documentation]] is not for you, you might find it more appealing to walk through a simple METAL analysis. | + | Many people find that it easiest to learn by example. So, if reading through our ''extensive'' [[METAL Documentation|documentation]] is not for you, you might find it more appealing to walk through a simple METAL analysis. |
| − | == The Glucose Data == | + | == The Glucose Data == |
| − | This example examines evidence for association between fasting glucose levels and genetic markers in the [http://www.sph.umich.edu/csg/abecasis/publications/18521185.html G6PC2] (chr. 2), GCK (chr. 7) and [http://www.sph.umich.edu/csg/abecasis/publications/19060907.html MTNR1B] (chr. 11) regions. It uses results from 3 genomewide association studies: [http://www.sph.umich.edu/csg/abecasis/publications/17463248.html FUSION], [http://www.sph.umich.edu/csg/abecasis/publications/PLOS-Obesity-Scan.html SardiNIA] and [http://www.ncbi.nlm.nih.gov/pubmed/17463246 DGI]. Genetic variants in the three loci impact fasting glucose levels and, in the case of MTRN1B, also impact the risk of type 2 diabetes. | + | This example examines evidence for association between fasting glucose levels and genetic markers in the [http://www.sph.umich.edu/csg/abecasis/publications/18521185.html G6PC2] (chr. 2), GCK (chr. 7) and [http://www.sph.umich.edu/csg/abecasis/publications/19060907.html MTNR1B] (chr. 11) regions. It uses results from 3 genomewide association studies: [http://www.sph.umich.edu/csg/abecasis/publications/17463248.html FUSION], [http://www.sph.umich.edu/csg/abecasis/publications/PLOS-Obesity-Scan.html SardiNIA] and [http://www.ncbi.nlm.nih.gov/pubmed/17463246 DGI]. Genetic variants in the three loci impact fasting glucose levels and, in the case of MTRN1B, also impact the risk of type 2 diabetes. |
| − | You can download a copy of the input files used in this example analysis from the [http://www.sph.umich.edu/csg/abecasis/Metal/download/ METAL Download Page]. | + | You can download a copy of the input files used in this example analysis from the [http://www.sph.umich.edu/csg/abecasis/Metal/download/ METAL Download Page]. |
| + | |||
| + | == Input Files == | ||
| + | |||
| + | Initially, each of the three studies analyzed association between fasting glucose levels and genotyped and imputed variants in each of the three loci. Study specific results are stored in the following files: | ||
| + | |||
| + | {| width="50%" border="0" cellpadding="1" cellspacing="1" | ||
| + | |+ Input Files with Single Study Results | ||
| + | |- | ||
| + | | STUDY | ||
| + | | INPUT FILE | ||
| + | | FILE SIZE | ||
| + | |- | ||
| + | | [http://www.sph.umich.edu/csg/abecasis/publications/17463248.html FUSION] | ||
| + | | MAGIC_FUSION_Results.txt.gz | ||
| + | | 46 kb | ||
| + | |- | ||
| + | | [http://www.sph.umich.edu/csg/abecasis/publications/PLOS-Obesity-Scan.html SardiNIA] | ||
| + | | magic_SARDINIA.tbl | ||
| + | | 188 kb | ||
| + | |- | ||
| + | | [http://www.ncbi.nlm.nih.gov/pubmed/17463246 DGI] | ||
| + | | DGI_three_regions.txt | ||
| + | | 188 kb | ||
| + | |} | ||
| + | |||
| + | <br> | ||
| + | |||
| + | Although some effort was made to harmonize analysis strategies (for example, by excluding individuals with a diagnosis of diabetes as well as other individuals with elevated fasting glucose levels) | ||
Revision as of 06:58, 30 March 2010
Learning by Example
Many people find that it easiest to learn by example. So, if reading through our extensive documentation is not for you, you might find it more appealing to walk through a simple METAL analysis.
The Glucose Data
This example examines evidence for association between fasting glucose levels and genetic markers in the G6PC2 (chr. 2), GCK (chr. 7) and MTNR1B (chr. 11) regions. It uses results from 3 genomewide association studies: FUSION, SardiNIA and DGI. Genetic variants in the three loci impact fasting glucose levels and, in the case of MTRN1B, also impact the risk of type 2 diabetes.
You can download a copy of the input files used in this example analysis from the METAL Download Page.
Input Files
Initially, each of the three studies analyzed association between fasting glucose levels and genotyped and imputed variants in each of the three loci. Study specific results are stored in the following files:
| STUDY | INPUT FILE | FILE SIZE |
| FUSION | MAGIC_FUSION_Results.txt.gz | 46 kb |
| SardiNIA | magic_SARDINIA.tbl | 188 kb |
| DGI | DGI_three_regions.txt | 188 kb |
Although some effort was made to harmonize analysis strategies (for example, by excluding individuals with a diagnosis of diabetes as well as other individuals with elevated fasting glucose levels)
