MR-MEGA | University of Tartu Institute of Genomics

Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
    +372 740 9959
    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
    Faculty address: 
    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
Faculty address: 
Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
    +372 737 6440
    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
    Faculty phone: 
    +372 737 5582
    Faculty address: 
    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
    Faculty phone: 
    +372 737 6310
    Faculty address: 
    J. Liivi 4, 50409 Tartu
  • Institute of Psychology
    Faculty phone: 
    +372 737 5902
    Faculty address: 
    Näituse 2, 50409 Tartu
  • School of Law
    Faculty phone: 
    +372 737 5390
    Faculty address: 
    Näituse 20–324, 50409 Tartu
  • Institute of Social Studies
    Faculty phone: 
    +372 737 5188
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Narva College
    Faculty phone: 
    +372 740 1900
    Faculty address: 
    Raekoja plats 2, 20307 Narva
  • Pärnu College
    Faculty phone: 
    +372 445 0520
    Faculty address: 
    Ringi 35, 80012 Pärnu
Faculty of Medicine
Faculty phone: 
+372 737 5326
Faculty address: 
Ravila 19, 50411 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5326
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Biomedicine and Translational Medicine
    Faculty phone: 
    +372 737 4210
    Faculty address: 
    Biomeedikum, Ravila 19, 50411 Tartu
  • Institute of Pharmacy
    Faculty phone: 
    +372 737 5286
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Dentistry
    Faculty phone: 
    +372 731 9856
    Faculty address: 
    Raekoja plats 6, 51003 Tartu
  • Institute of Clinical Medicine
    Faculty phone: 
    +372 737 5323
    Faculty address: 
    L. Puusepa 8, 50406 Tartu
  • Institute of Family Medicine and Public Health
    Faculty phone: 
    +372 737 4190
    Faculty address: 
    Ravila 19, 50411 Tartu
  • Institute of Sport Sciences and Physiotherapy
    Faculty phone: 
    +372 737 5360
    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
+372 737 5820
Faculty address: 
Vanemuise 46–208, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
    Faculty phone: 
    +372 737 5445
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Estonian Marine Institute
    Faculty phone: 
    +372 671 8902
    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
    W. Ostwaldi 1, 50411 Tartu
  • Institute of Chemistry
    Faculty phone: 
    +372 737 5261
    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
    Faculty phone: 
    +372 737 5860
    Faculty address: 
    J. Liivi 2, 50409 Tartu
  • Institute of Molecular and Cell Biology
    Faculty phone: 
    +372 737 5011
    Faculty address: 
    Riia 23, 23b–134, 51010 Tartu
  • Tartu Observatory
    Faculty phone: 
    +372 737 4510
    Faculty address: 
    Observatooriumi 1, Tõravere, 61602 Tartumaa
  • Institute of Technology
    Faculty phone: 
    +372 737 4800
    Faculty address: 
    Nooruse 1, 50411 Tartu
  • Institute of Ecology and Earth Sciences
    Faculty phone: 
    +372 737 5835
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Institutions
  • Library
    Faculty phone: 
    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
    Faculty phone: 
    +372 737 5581
    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
    Faculty phone: 
    +372 737 6076
    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
  • Administrative Office
    Faculty phone: 
    +372 737 5606
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Centre for Entrepreneurship and Innovation
    Faculty phone: 
    +372 737 6339
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • University Office in Tallinn
    Faculty phone: 
    +372 737 6600
    Faculty address: 
    Teatri väljak 3, 10143 Tallinn
  • Estates Office
    Faculty phone: 
    +372 737 5137
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
    Faculty phone: 
    +372 737 5125
    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
    Faculty phone: 
    +372 737 6215
    Faculty address: 
    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
    Faculty phone: 
    +372 737 6000, IT-help: +372 737 5500
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Human Resources Office
    Faculty phone: 
    +372 737 5145
    Faculty address: 
    Ülikooli 18, rooms 302 and 304, 50090 Tartu
  • Internal Audit Office
    Faculty address: 
    Ülikooli 17–103, 51005 Tartu
  • Marketing and Communication Office
    Faculty phone: 
    +372 737 5687
    Faculty address: 
    Ülikooli 18, rooms 102, 104, 209, 210, 50090 Tartu
  • Office of Academic Affairs
    Faculty phone: 
    +372 737 5620
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Procurement Office
    Faculty phone: 
    +372 737 6632
    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Rector's Strategy Office
    Faculty phone: 
    +372 737 5600
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • Student Council
    Faculty phone: 
    +372 737 5400
    Faculty address: 
    Ülikooli 18b, 51005 Tartu
Other Units
  • University of Tartu Academic Sports Club
    Faculty phone: 
    +372 737 5371
    Faculty address: 
    Ujula 4, 51008 Tartu
  • Tartu Student Village
    Faculty phone: 
    +372 740 9959
    Faculty address: 
    Narva mnt 25, 51013 Tartu
  • Tartu Students’ Club
    Faculty phone: 
    +372 730 2400
    Faculty address: 
    Kalevi 24, 51010 Tartu
  • University of Tartu Press
    Faculty phone: 
    +372 737 5945
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Tartu University Hospital
    Faculty address: 
    L. Puusepa 1a, 50406 Tartu
  • University of Tartu Foundation
    Faculty phone: 
    +372 737 5852
    Faculty address: 
    Ülikooli 18, 50090 Tartu
  • View all other units

MR-MEGA

INTRODUCTION

MR-MEGA (Meta-Regression of Multi-Ethnic Genetic Association) is a tool to detect and fine-map complex trait association signals via trans-ethnic meta-regression.  This approach uses genome-wide metrics of diversity between populations to derive axes of genetic variation via multi-dimensional scaling [Purcell 2007].  Allelic effects of a variant across GWAS, weighted by their corresponding standard errors, can then be modelled in a linear regression framework, including the axes of genetic variation as covariates.  The flexibility of this model enables partitioning of the heterogeneity into components due to ancestry and residual variation, which would be expected to improve fine-mapping resolution.

Questions and suggestions conserning the method should be sent to: apmorris [ät] liverpool.ac.uk

 

CITATION 

Please cite the paper:

Mägi R, Horikoshi M, Sofer T, Mahajan A, Kitajima H, Franceschini N, McCarthy MI; COGENT-Kidney Consortium, T2D-GENES Consortium, Morris AP. Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution. Hum Mol Genet. 2017 Sep 15;26(18):3639-3650

 

DOWNLOAD

MR-MEGA ver. 0.1.5

Please note that current version is still beta version and may contain errors. In case of any problems, please write to reedik.magi [ät] ut.ee

Some additional tools:

fixP.r
manh.r
qq.r

 

As the current C++ library enables to calculate p-values>1e-14, you can use fixP.r script to recalculate p-values in R  based on chisq and ndf values down to p-values>1e-325. This script is not necessary for creating MANH and QQ plots as these scripts will do the same calculation independently. 

To run the script, use following command:

R --slave --vanilla < fixP.r

If your result file is not mrmega.result, then you can also change input and output files of the script by:

R --slave --vanilla --args input=inputfilename out=outputfilename < fixP.r

 

Manhattan and QQ plots can be created with accompanied R scripts.

R --slave --vanilla < manh.r

R --slave --vanilla < qq.r

By default they expect input file name "mrmega.result" and they create output files: "mrmega.result.qq_assoc.png",  "mrmega.result.qq_ancest.png" "mrmega.result.qq_resid.png" and "mrmega.result.manh.png". Different names can be used as:

R --slave --vanilla --args input=inputfilename out=outputfilename < MANH.R

R version 2.9.0 or later must be used with png support

 

INSTALLATION

Copy MR-MEGA_v*.zip file into your computer, unzip the file: 

unzip MRMEGA_v*.zip 

To compile MR-MEGA program, use command: 

make 

in the folder where files have been unpacked. The program can be run by typing: 

./MR-MEGA

 

INPUT FILES FOR MR-MEGA

For running MR-MEGA you have to create an input file (default name “mr-mega.in”), which contains the list of all study files. The should have each results' file on separate row. 

Sample “MR-MEGA.in” file:

Pop1.txt.gz
Pop2.txt.gz

Pop3.txt.gz
Pop4.txt.gz
Pop5.txt.gz
Pop6.txt.gz
Pop7.txt.gz
Pop8.txt.gz

 

Each GWA study file has mandatory column headers:

1) MARKERNAME – snp name

2) EA – effect allele

3) NEA – non effect allele

4) OR - odds ratio

5) OR_95L - lower confidence interval of OR

6) OR_95U - upper confidence interval of OR

7) EAF – effect allele frequency

8) N - sample size

9) CHROMOSOME  - chromosome of marker

10) POSITION - position of marker

 

In case of quantitative trait:

4) BETA – beta

5) SE – std. error

Study files might also contain column:

11) STRAND – marker strand (if the column is missing then program expects all markers being on positive strand)

 

Sample study file (NB! This file is a quantitative trait one and MR-MEGA has to be run with --qt command line option):

MARKERNAME STRAND CHROMOSOME POSITION IMP EA NEA EAF N BETA SE
rs12565286 + 1 761153 0 G C 0.3 1200 -0.02 0.0403
rs2977670 + 1 763754 0 C G 0.23 1200 -0.01 0.40612
rs12138618 + 1 790098 0 G A 0.97 1200 -0.07 0.37
rs3094315 + 1 792429 0 G A 0.01 1199 0.0258 0.1012
rs3131968 + 1 794055 0 G A 0.27 1200 -0.373 0.0101
rs2519016 + 1 805811 0 T C 0.04 1200 0.26 0.3472
rs12562034 + 1 808311 0 G A 0.65 1200 0.0092 0.2


Input files must be either tab or space delimited. Files must not have empty columns as multiple separators are treated as one. Files may contain additional columns, which are not used by MR-MEGA.

 
 

RUNNING Mr-MEGA

Command line options: 

./MR-MEGA  [--name_pos <string>] ...  [--name_chr <string>] ... 

              [--name_n <string>] ...  [--name_strand <string>] ... 

              [--name_or_95u <string>] ...  [--name_or_95l <string>] ... 

              [--name_or <string>] ...  [--name_se <string>] ... 

              [--name_beta <string>] ...  [--name_eaf <string>] ... 

              [--name_nea <string>] ...  [--name_ea <string>] ... 

              [--name_marker <string>] ...  [-f <string>] ...  [--pc <int>]

              [-t <double>] [--no_std_names] [--debug] [--qt] [--gco]

              [--gc] [--no_alleles] [-m <string>] [-o <string>] [-i

              <string>] [--] [--version] [-h]

 

 

Where: 

 

   --name_pos <string>  (accepted multiple times)

     Alternative header to position column. Default POSITION

 

   --name_chr <string>  (accepted multiple times)

     Alternative header to chromosome column. Default CHROMOSOME

 

   --name_n <string>  (accepted multiple times)

     Alternative header to sample size column. Default N

 

   --name_strand <string>  (accepted multiple times)

     Alternative header to strand column. Default STRAND

 

   --name_or_95u <string>  (accepted multiple times)

     Alternative header to upper 95 CI of odds ratio column. Default OR_95U

 

   --name_or_95l <string>  (accepted multiple times)

     Alternative header to lower 95 CI of odds ratio column. Default OR_95L

 

   --name_or <string>  (accepted multiple times)

     Alternative header to odds ratio column. Default OR

 

   --name_se <string>  (accepted multiple times)

     Alternative header to standard error column. Default SE

 

   --name_beta <string>  (accepted multiple times)

     Alternative header to effect column. Default BETA

 

   --name_eaf <string>  (accepted multiple times)

     Alternative header to effect allele frequency column. Default EAF

 

   --name_nea <string>  (accepted multiple times)

     Alternative header to other allele column. Default NEA

 

   --name_ea <string>  (accepted multiple times)

     Alternative header to effect allele column. Default EA

 

   --name_marker <string>  (accepted multiple times)

     Alternative header to marker name column. Default MARKERNAME

 

   -f <string>,  --filter <string>  (accepted multiple times)

     Set a filtering based on column name. It needs 3 arguments: column

     name, equation [>,<,>=,<=,==,!=], numeric filter value. Multiple

     filters can be set. Please note that UNIX may require using '\' before

     '<' and '>' signs. Column names are not case sensitive. (Example:

     INFO\>0.4)

 

   --pc <int>

     This specifies the number od PC to use in regression. Default = 4. Please note that the PC count must be < cohort count - 2. Therefore, if five cohorts have been used in the analyse, then the maximum number of PC-s can be two!

 

   -t <double>,  --threshold <double>

     The p-value threshold for showing direction. Default = 1

 

   --no_std_names

     Default column names are not used. All columns must be be defined by

     user

 

   --debug

     Debug mode on (default OFF)

 

   --qt

     Use this option, if trait is quantitative (columns BETA & SE). Default

     is binary trait (columns OR, OR95_U, OR_95_L)

 

   --gco

     Use second genomic control correction on output file

 

   --gc

     Use genomic control correction on input files

 

   --no_alleles

     No allele information has been given. Expecting always the same EA

 

   -m <string>,  --map <string>

     This specifies map file

 

   -o <string>,  --out <string>

     This specifies output root. By default mrmega

 

   -i <string>,  --filelist <string>

     Specify studies' result files. Default = mrmega.in

 

   --,  --ignore_rest

     Ignores the rest of the labeled arguments following this flag.

 

   --version

     Displays version information and exits.

 

   -h,  --help

     Displays usage information and exits.

 

 

OUTPUT FILES

MR-MEGA generates two output files: *.result and *.log

Results file contains following columns:


MarkerName - unique marker identification across input files

Chromosome - chromosome of marker

Position - physical position in chromosome of marker

EA - allele, which effect was measured across input files

NEA - other allele

EAF - average effect allele frequency (weighted by the samplesize of each input file)

Nsample - total number of samples

Ncohort - total number of cohorts, where the marker was present

Effects - effect direction across cohorts (+ if the effect allele effect was positive, - if negative, 0 if the effect was zero, ? if marker was not available in cohort)

beta_0 - effect of first PC of meta-regression

se_0 - stderr of the effect of first PC of meta-regression

(beta_1)

(se_1)

(...)

chisq_association - chisq value of the association

ndf_association - number of degrees of freedom of the association

P-value_association - p-value of the association

chisq_ancestry_het - chisq value of the heterogeneity due to different ancestry

ndf_ancestry_het - ndf of the heterogeneity due to different ancestry

P-value_ancestry_het - p-value of the heterogeneity due to different ancestry

chisq_residual_het - chisq value of the residual heterogeneity

ndf_residual_het - ndf of the residual heterogeneity

P-value_residual_het - p-value of the residual heterogeneity

lnBF - log of Bayes factor

Comments - reason why marker was not analysed