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1. Introduction
2. Basic information
3. Download and general notes
4. Command reference table
5. Basic usage/data formats
6. Data management
7. Summary stats
8. Inclusion thresholds
9. Population stratification
10. IBS/IBD estimation
11. Association
12. Family-based association
13. Permutation procedures
14. LD calculations
15. Multimarker tests
16. Conditional haplotype tests
17. Proxy association
18. Imputation (beta)
19. Dosage data
20. Meta-analysis
21. Annotation
22. LD-based results clumping
23. Gene-based report
24. Epistasis
25. Rare CNVs
26. Common CNPs
27. R-plugins
28. Annotation web-lookup
29. Simulation tools
30. Profile scoring
31. ID helper
32. Resources
33. Flow-chart
34. Miscellaneous
35. FAQ & Hints
36. gPLINK
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Getting started with PLINK
This page contains some important information on learning to use PLINK
and how to handle any problems you encounter.
We suggest that after downloading PLINK
you first try the tutorial. This will
familiarize you with the basic PLINK commands.
Citing PLINK
If you use PLINK in any published work, please cite both the software
(as an electronic resource/URL) and the manuscript describing the
methods.
Package: PLINK (including version number)
Author: Shaun Purcell
URL: http://pngu.mgh.harvard.edu/purcell/plink/
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR,
Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based
linkage analysis. American Journal of Human Genetics, 81.
Reporting problems, bugs and questions
If you have any problems with PLINK or would like to report a bug,
please follow these steps:
PLEASE READ THIS SECTION BEFORE E-MAILING!
When an analysis does not report the results you expect, or when PLINK
seemingly gives different answers to previous versions or to other
software packages, or the last time you ran it, etc, please feel me to
e-mail me
plink AT chgr DOT mgh DOT harvard DOT edu
but also please consider the following before doing so:
- Please first check the Frequently Asked Questions
list to see if your question has already been answered
- Please check the LOG file, it often contains important
information. For example, did it filter out some individuals based on
genotyping rate or missing phenotype/sex information which you were
not expecting?
- Please check the format of your data: is it plain text? does
each file have the correct number of rows, etc. Are the missing value
codes appropriate?
- Please recheck the web-documentation: sometimes the syntax of an
option may change.
- If the above steps do not resolve your problem, then please
e-mail me plink AT chgr dot mgh dot harvard dot edu (this is
different from the mailing list -- i.e. your e-mail will only be sent to me,
not the whole list). The more specific your e-mail, the easier it will be
for me to diagnose any problem or error. Please include:
- The whole LOG file(s)
- The type of machine you were using
- Ideally, please try to make some reduced dataset that
replicates the problem that you are able to send to me in a ZIP file,
so that I will be able to recreate the problem; any data sent to me
for these purposes will be immediately deleted after I have resolved
the problem.
HINT The more of the above steps you follow, the
more likely you are to receive a timely, useful response! If you
haven't heard within a week or so, please feel free to send a reminder
e-mail...
IMPORTANT I am willing and able to advise on the
use of specific features implemented in PLINK: to diagnose whether
they are working as intended and to give a generic description of a
procedure or method, if it is unclear from the web documentation. I'm
afraid I will not necessarily be able to give specific advice on any
one particular dataset, why you should use one method over another,
what it all means, etc...
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