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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. Multimarker tests
15. Conditional haplotype tests
16. Proxy association
17. Full imputation (beta)
18. LD-based results clumping
19. Epistasis
20. Copy Number Variation
21. R-plugins
22. SNP annotation lookup
23. Simulation tools
24. Profile scoring
25. Resources
26. Miscellaneous
27. FAQ & Hints
28. gPLINK
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Miscellaneous
This page details a collection of options and commands that did not
get proper mention elsewhere.
Output modifiers
One convenient filter is
--pfilter 1e-3
which will, for example, only report statistics with p-values less than 1e-3.
NOTE This is operation for the basic association
tests, but do not expect this to work for all methods that return a p-value.
To obtain -log10(p) values instead of p-values in the *adjusted file, add the
flag (this does not change the output of p-values in other files)
--log10
To fix the value of lambda used for the genomic control in
the *adjusted file, instead of estimating it from the data, use the
option, for example
--lambda 1.2
To obtain an extra set of columns that facilitates making a Q-Q plot
in the *.adjusted file, add the option
--qq-plot
This will work with either basic p-values, or with --log10 p-values.
Analyses with different species
In this respect, PLINK differentiates between species only in terms of
how many chromosomes there are, and which are sex-linked or
haploid. Several non-human species are supported, by adding each
analysis the extra flag
--dog
or
--horse
or
--cow
or
--sheep
Matrix of pairwise LD (genotype correlation)
Correlations based on genotype allele counts (i.e. w/out phasing, and
for founders only) can be obtained with the commands
plink --file mydata --r
or
plink --file mydata --r2
These both create a file called
plink.ld
with a list of R or R-squared values in it.
Filtering the output
By default, several filters on imposed on which pairwise calculations
are calculated and reported. To only analyse SNPs that are not more
than 10 SNPs apart, for example, use the option (default is 10 SNPs)
--ld-window 10
to specify a kb window in addition (default 1Mb)
--ld-window-kb 1000
and to report only values above a particular value (this only applies when the --r2
and not the --r command is used) (default is 0.2)
--ld-window-r2 0.2
The default for --ld-window-r2 is set at 0.2 to reduce the
size of output files when many comparisons are made: to get all pairs
reported, set --ld-window-r2 to 0.
Obtaining LD values for a specific SNP versus all others
To obtain all LD values for a set of SNPs versus one specific SNP, use the --ld-snp
command in conjunction with --r2. For example, to get a list of all values for
every SNP within 1Mb of rs12345, use the command
plink --file mydata
--r2
--ld-snp rs12345
--ld-window-kb 1000
--ld-window 99999
--ld-window-r2 0
The --ld-window and --ld-window-r2 commands effectively means that output
will be shown for all other SNPs within 1Mb of rs12345.
Obtaining a matrix of LD values
Alternatively, it is possible to add the --matrix option,
which creates a matrix of LD values rather than a list: in this case,
all SNP pairs are calculated and reported.
Haplotype-based LD calculations
A different command, --ld, instead takes two SNP IDs as
parameters and calculates the R-squared based on the four haplotype
frequencies: i.e. unlike the basic --r2 command, which is
based simply on the genotypic correlation, this involves phasing, just
for one particular pair of SNPs. For example:
plink --file mydata --ld rs12345 rs67890
No output files are generated apart from the LOG file, which
reports the estimated R-squared value:
LD information for SNP pair [ rs12345 rs67890 ]
r-sq = 0.944388
Again, these calculations are based only on founders.
Known issues
Development of PLINK is ongoing: as such, there is always
likely to be a list of features, listed here, that are only partialy
implemented, or have known problems not yet fixed. A list of known issues
can be found on the warnings page:
http://pngu.mgh.harvard.edu/purcell/plink/warnings.shtml
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