Command-line help
--help [flag name/prefix...]
When invoked with no parameters, --help provides a summary of all PLINK flags, starting with the main functions. This is long (over 1000 lines); we recommend you pipe the output through a terminal pager like Unix less or more, or dump it to a file with e.g.
plink --help > plink-help.txt
Alternatively, you can provide one or more flag names/prefixes to cause PLINK to only display information on the referenced flags, e.g.
[chrchang:~/plink-ng]$ plink --help abcd Z-gneome
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
--genome ['gz'] ['rel-check'] ['full'] ['unbounded'] ['nudge']
Generate an identity-by-descent report.
* It is usually best to perform this calculation on a marker set in
approximate linkage equilibrium.
* The 'rel-check' modifier excludes pairs of samples with different FIDs
from the final report.
* 'full' adds raw pairwise comparison data to the report.
* The P(IBD=0/1/2) estimator employed by this command sometimes yields
numbers outside the range [0,1]; by default, these are clipped. The
'unbounded' modifier turns off this clipping.
* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2)
estimates to a theoretically possible configuration.
* The computation can be subdivided with --parallel.
--ppc-gap <val> : Minimum number of base pairs, in thousands, between
informative pairs of markers used in --genome PPC test.
500 if unspecified.
--min <cutoff> : Specify minimum PI_HAT for inclusion in --genome report.
--max <cutoff> : Specify maximum PI_HAT for inclusion in --genome report.
No help entry for 'abcd'.
More precisely, for each parameter you pass to --help, PLINK will first search for an exact flag name match; if it fails to find one, it will then search for exact prefix matches; and if it also fails to find any of those, it will search for Damerau-Levenshtein distance 1 matches (note the 'Z-gneome' misspelling above). (The "Quick index search" on this webpage's sidebar uses the same logic.)
If --help is used with other flags (other than --script and --rerun), it causes everything before it on the command line to be ignored, and everything after it to be treated as --help parameters. This is convenient when you've forgotten exactly how a flag works while in the middle of typing a long command: you can put your help request at the end of the unfinished command, and then retrieve your unfinished command line with the up arrow (in most shells, anyway).
[chrchang:~/plink-ng]$ plink --bfile test_data --hwe 1e-5 midp --help --pca
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
--help present, ignoring other flags.
--pca {count} ['header'] ['tabs'] ['var-wts']
Calculates a variance-standardized relationship matrix (use
--make-rel/--make-grm-gz/--make-grm-bin to dump it), and extracts the top
20 principal components.
* It is usually best to perform this calculation on a marker set in
approximate linkage equilibrium.
* You can change the number of PCs by passing a numeric parameter.
* The 'header' modifier adds a header line to the .eigenvec output file.
(For compatibility with the GCTA flag of the same name, the default is no
header line.)
* The 'tabs' modifier causes the .eigenvec file(s) to be tab-delimited.
* The 'var-wts' modifier requests an additional .eigenvec.var file with PCs
expressed as variant weights instead of sample weights.
--pca-cluster-names <...> : These can be used individually or in combination
--pca-clusters <fname> to define a list of clusters to use in the basic
--pca computation. (--pca-cluster-names expects
a space-delimited sequence of cluster names,
while --pca-clusters expects a file with one
cluster name per line.) All samples outside
those clusters will then be projected on to the
calculated PCs.
[chrchang:~/plink-ng]$ plink --bfile test_data --hwe 1e-5 midp --pca ...
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