colocalization

This tool calculates the colocalization score or PPV of a given complex set. It requires localization data for the corresponding proteome.

Call the tool without any command line arguments to get detailed information about the parameters for this program.

See also:

Example calls

cmdline.sh colocalization -i data/complexes/mips_complexes.txt -loc data/localization/huh_loc_070804.txt -nomiss -nonweighted

cmdline.sh colocalization -i data/complexes/mips_complexes.txt -loc data/localization/huh_loc_070804.txt -nomiss -ppv -outtype 1

cmdline.sh colocalization -i data/complexes/mips_complexes.txt -loc data/localization/huh_loc_070804.txt -outtype 2















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Parameters

Required parameters
-i file containing the complex set which will be evaluated
-loc file containing localization data
Optional parameters
-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
-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
-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
-ppv Calculate the colocalization PPV instead of the colocalization score (see: Complex set evaluation)
to be continued
Input/Output



ProCope documentation