PLINK: Whole genome data analysis toolset plink...
Last original PLINK release is v1.07 (10-Oct-2009); PLINK 1.9 is now available for beta-testing

Whole genome association analysis toolset

Introduction | Basics | Download | Reference | Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association | Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | ID helper | Resources | Flow chart | Misc. | FAQ | gPLINK

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
 

SNP simulation routine

PLINK provides an interface to a very simplistic SNP simulation routine, designed to generate large SNP datasets for population-based, case/control studies. This function is largely intended as a convenience function for generating data to prototype new methods, comparing the power of different approaches, etc, rather than producing realistic whole genome data. Critically, all SNPs simulated are unlinked and in linkage equilibrium.

Basic usage

The basic command to simulate a SNP data file is the --simulate option,
./plink --simulate wgas.sim --make-bed --out sim1

which takes as a parameter the name of a file (here wgas.sim) that describes the to-be-simulated data.

The simulation file wgas.sim is as follows:
     100000  null      0.00 1.00  1.00 1.00
     100     disease   0.00 1.00  2.00 mult
These files can have 1 or more rows, where each row has exactly five fields, as follows
     Number of SNPs in this set
     Label of this set of SNPs
     Lower allele frequency range
     Upper allele frequency range
     Odds ratio for disease, heterozygote
     Odds ratio for disease, homozyygote (or "mult")
Specifying mult implies a multiplicative risk for the homozygote, e.g. 2*2=4 in the above example.

Given this file, PLINK would generate 100,000 SNPs with no association with disease. Each SNP would have its own population allele frequency, generated as a uniform number between, in this case, 0.00 and 1.00. In addition, 100 extra SNPs will be simulated that are associated with disease (population odds ratio of 2.00).

The names of each SNP would follow from the label (which must be unqiue), with a number appended, e.g.
     null_0
     null_1
     null_2
     ...
     disease_99
An exception is that if a set only contains a single SNP, nothing is appended to the label. This is useful in generating multiple samples from the same population, as described below.

Obviously, a uniform allele frequency range is not realistic: one could instead specify a series of bins to enrich for rarer SNPs, if so desired, to build a more realistic spectrum of allele frequencies (not that the example below is meant to be more realistic).
     20000  nullA     0.00 0.05  1.00 1.00
     10000  nullB     0.05 0.10  1.00 1.00
      5000  nullC     0.10 0.20  1.00 1.00
     10000  nullD     0.20 0.99  1.00 1.00
      ... 
As well as generating the actual data, the --simulate outputs to the LOG file the following:
     Reading simulation parameters from [ wgas.sim ]
     Writing SNP population frequencies to [ plink.simfreq ]
     Read 2 sets of SNPs, specifying 100100 SNPs in total
     Simulating 100 cases and 100 controls
     Assuming a disease prevalence of 0.01
The plink.simfreq file is described below. By default, 100 cases and 100 controls are generated. This can be changed with the command-line options
     --simulate-ncases 5000
and
     --simulate-ncontrols 5000
for example. Likewise, the default disease prevalence is assumed to be 0.01. This can be changed with
     --simulate-prevalence 0.05
for example.

In the example above, the simulated data were directly saved to a binary fileset: this need not be the case. For example, any other analysis command could instead have been applied, e.g. --simulate acts just like --file or --bfile:
./plink --simulate wgas.sim --assoc

although the actual simulated data would be subsequently lost of course.

Hint This tool only generates individuals drawn from a homogeneous population, but you can easily imagine using several --simulate runs then using PLINK commands to merge the resulting files to specify more complex scenarios, e.g. representing population stratification, allelic heterogeneity, etc.

The command
     --simulate-label POP1
will append the text label POP1 to the ID of each individual generated. This can be useful when generating and subsequently merging multiple simulated samples (so unique IDs can be specified across all samples).

Specification of LD between marker and causal variant

It is also possible to simulate data in which the observed marker SNP is only in incomplete LD with the actual causal allele. This is achieved with either the --simulate-tags or --simulate-haps options, e.g.
plink --simulate ld.sim --simulate-tags

PLINK now expects 9 fields instead of 6 in the simulation file: namely,
     Number of SNPs in this set
     Label of this set of SNPs
     Lower allele frequency range, causal variant
     Upper allele frequency range, causal variant
     Lower allele frequency range, marker
     Upper allele frequency range, marker
     Marker / causal variant LD (D-prime)
     Odds ratio for disease, heterozygote causal variant
     Odds ratio for disease, homozyygote causval variant, (or "mult")
For example,
     5    snp    0.05 0.05      0.5 0.5    0.5   2 mult
Implies 5 CVs, each of 5% MAF and 2-fold multiplicative effect size (each in linkage equilibrium still) but with 10 additional markers, each of 50% MAF, each in complete LD with D'=0.5 with their respective CV (i.e. pairs of markers are simulated). The command
plink --simulate ld.sim --simulate-tags --assoc

will therefore generate only 10 SNPs, that are the markers that tag the CVs, i.e. note the frequency of these variants is around 50%
 CHR     SNP         BP   A1      F_A      F_U   A2        CHISQ            P           OR
   1   snp_0          1    D    0.474   0.5045    d        3.723      0.05368       0.8851
   1   snp_1          2    D    0.484   0.4985    d       0.8413        0.359       0.9436
   1   snp_2          3    D    0.493   0.4775    d       0.9618       0.3267        1.064
   1   snp_3          4    D    0.486    0.494    d       0.2561       0.6128       0.9685
   1   snp_4          5    D   0.4925   0.5005    d        0.256       0.6129       0.9685
In contrast, the related command
plink --simulate ld.sim --simulate-haps --assoc

will output both the causal variant and the marker, with _M appended to the marker name:
 CHR     SNP         BP   A1      F_A      F_U   A2        CHISQ            P           OR
   1   snp_0          1    D   0.0995    0.044    d        46.25    1.042e-11        2.401
   1 snp_0_M          2    B   0.4885    0.494    A        0.121       0.7279       0.9782
   1   snp_1          3    D   0.0875    0.044    d         30.8    2.853e-08        2.083
   1 snp_1_M          4    B   0.4815   0.5055    A        2.304        0.129       0.9084
   1   snp_2          5    D    0.088   0.0575    d        13.79    0.0002044        1.582
   1 snp_2_M          6    B    0.459   0.5115    A        11.03    0.0008943       0.8103
   1   snp_3          7    D   0.0965    0.047    d        36.79    1.316e-09        2.166
   1 snp_3_M          8    B   0.5005    0.491    A        0.361       0.5479        1.039
   1   snp_4          9    D    0.093   0.0535    d        22.98    1.634e-06        1.814
   1 snp_4_M         10    B   0.4895    0.496    A        0.169        0.681       0.9743
WARNING Again, please note that this procedure does not produce anything like realistic patterns of LD as one would expect to observe in whole genome datasets: rather, this simply simulates pairs of markers, for which there is LD within, but not between, pairs.

Resimulating a sample from the same population

The --simulate command also generates the file plink.simfreq. This records, for each SNP of the two sets, null and disease from the wgas.sim example, the actual allele frequency chosen for that particular SNP when simulating the data. For example,
     1 null_0   0.1885 0.1885       1.00 1.00
     1 null_1   0.424675 0.424675   1.00 1.00
     1 null_2   0.12797 0.12797     1.00 1.00
     1 null_3   0.544394 0.544394   1.00 1.00
     1 null_4   0.938641 0.938641   1.00 1.00
     ....
Conveniently, this information is output in the same format as the original simulation file: note how the upper and lower allele frequency range is converged to specify a particular value, i.e. the first row shows a range of 0.1885 to 0.1885, i.e. effectively forcing the allele frequency for the first SNP to be 0.1885. This can be useful, as to generate a new independent dataset from the same population as the first, you would simply use the plink.simfreq output file, as input for a new --simulate command, see below.

Putting this together, one might imagine setting up a simple screen/replicate simulation design: first we generate the original WGAS screening data
./plink --simulate wgas.sim --make-bed --out screen

run our association test
./plink --bfile screen --assoc

and extract a list of significant SNPs (here using the Unix gawk command, to filter on the p-value column, 9)
gawk ' NR>1 && $9 < 1e-3 { print $2 } ' plink.assoc > positives

and then generate and test these same SNPs in an independent sample
./plink --simulate screen.simfreq --extract positives --assoc --out replication

etc. By labeling true disease SNPs and null SNPs sensibly as above, you can tell how many true positives and false positives appear at the screening and the replication stages, e.g. using Unix bash shell scripting to summarise results:
   t=1e-3
   s0=`fgrep null plink.assoc | gawk ' $9 < t ' t=$t | wc -l`
   s1=`fgrep disease plink.assoc | gawk ' $9 < t ' t=$t | wc -l`
   echo "Detected $s1 true positives and $s0 false positives in screening"

   t=1e-2
   s0=`fgrep null replication.assoc | gawk ' $9 < t ' t=$t | wc -l`
   s1=`fgrep disease replication.assoc | gawk ' $9 < t ' t=$t | wc -l`
   echo "Of these, $s1 true positives and $s0 false positives replicate"

Simulating a quantitative trait

To simulate a quantitative trait based on one or more unlinked SNPs, use the command
plink --simulate-qt myfile.sim --simulate-n 1000

where myfile.sim is similar in format to the file taken by the standard --simulate option, except the two final fields represent the additive genetic variance, and the ratio of dominance to additive effects, e.g. if myfile.sim is
 10 qtl 0.05 0.95  0.01 0
then
plink --simulate-qt myfile.sim

will generate ten unlinked QTLs, with allele frequency between 0.05 and 0.95 for the trait-increasing allele. In each case, the effect size will be calculated to give a population variance explained of 0.01. The final 0 indicates the effects are additive (1 means complete dominance, -1 means complete recessive). In this case, the output is
      Reading QT simulation parameters from [ sim1.sim ]
      Writing SNP population frequencies to [ plink.simfreq ]
      Read 1 sets of SNPs, specifying 10 SNPs in total
      Simulating QT for 1000 individuals 
      Total QTL variance is 0.1
      Simulating disease variants (direct association)
This lists the total population variance explained by all QTLs -- in this case, 0.1. If the variance explained is greater than 1, an error message will be reported.

If the --assoc command were also specified along with the above command, standard QT association tests would be performed for each simulate SNP, e.g. plink.qassoc:
      CHR     SNP         BP    NMISS       BETA         SE         R2        T            P 
        1   qtl_0          1     1000     0.1988    0.05263     0.0141    3.777    0.0001678 
        1   qtl_1          2     1000    0.09956    0.04623   0.004626    2.154      0.03151 
        1   qtl_2          3     1000    -0.2101     0.0683   0.009391   -3.076     0.002156 
        1   qtl_3          4     1000      0.186    0.04728    0.01528    3.935    8.911e-05 
        1   qtl_4          5     1000     0.1489    0.04714   0.009899    3.159     0.001632 
        1   qtl_5          6     1000    -0.1854    0.04569    0.01623   -4.057    5.351e-05 
        1   qtl_6          7     1000     0.2287    0.05745    0.01563    3.981    7.355e-05 
        1   qtl_7          8     1000    -0.2011    0.08519   0.005551    -2.36      0.01845 
        1   qtl_8          9     1000      0.166    0.04337    0.01446    3.827    0.0001377 
        1   qtl_9         10     1000    -0.1007    0.04773   0.004437   -2.109       0.0352 
showing R2 (variance explained) values around 0.01, as expected, with the sampling variation due to sample of 1000 individuals (the default sample size, if --simulate-n is not specified).

The additional commands such as --simulate-label and --simulate-tags, etc, can be used with the --simulate-qt option.
 
This document last modified Saturday, 10-Oct-2009 10:42:44 EDT