Required parameters |
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-i |
file containing the complex set which will be evaluated
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-loc |
file containing localization data |
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Optional parameters |
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-outtype |
Defines what output will be generated by the tool:
- 0 - a single averaged score for the whole complex set
will be printed out
- 1 - one score for each complex will be printed out
- 2 - a network will be printed, this network contains
one edge for each pair of proteins which are in the same complex and
colocalized
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-nomiss |
If this flag is set, complexes where no localization
data are present for any proteins will not get a
score of zero. Instead the score of this complex will be completely
ignored. This is only relevant for -outtype 0 |
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-nonweighted |
If
this flag is set, an unweighted average will be calculated over the
complex set. If it is not set, each score will be weighted by the size
of the respective complex for averaging. This is only relevant for
-outtype 0 |
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-ppv |
Calculate the colocalization PPV instead of the
colocalization score (see: Complex set evaluation) |
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to be continued |
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Input/Output |
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