complexmanipulate
This tool contains three methods to manipulate complex sets:
- score cutoff - delete complexes whose average inner-complex
edge score is below a given threshold (requires a scores network)
- decompose - delete edges below a given
threshold, complexes may decompose into subcomplexes (requires
a scores network)
- size cutoff - delete all complexes which consist of more or
less than a given number of proteins
Call the tool without any command line arguments to get detailed
information about the parameters for this program.
See also:
Example calls
- delete all complexes from the MIPS reference complex set whose average complex score is below 0.5 (
-i
, -scorecut
)
- use the bootstrap scores network for this (
-scorenet
)
- output the result to a given file (
-o
)
cmdline.sh complexmanipulate -i data/complexes/mips_complexes.txt
-o testout -scorecut 0.5 -scorenet data/scores/bootstrap_combined.txt.gz
- decompose the MIPS reference set with a threshold of 0.5 (see above,
-decompose
)
- afterwards delete all complexes with less then 2 members (
-sizecut
)
cmdline.sh complexmanipulate -i data/complexes/mips_complexes.txt
-o testout -decompose 0.5 -scorenet
data/scores/bootstrap_combined.txt.gz -size 2-