generatescores
Creates PPI score networks using a given score method. Note that
boostrap scores cannot
be calculated with this tool as several consequtive steps are required
for that method.
Call the tool without any command line arguments to get detailed
information about the parameters for this program.
See also:
Example calls
- use the Gavin et al., 2006 purification
dataset (
-p
)
- calculate socio affinity scores (
-score socio
)
- only output scores >= 5.0 (
-c
)
- write the output to a file (
-o
)
cmdline.sh generatescores -p
data/purifications/gavin_raw.txt -score socio -c 5.0 -o socios.net
- this time calculate Purification enrichment scores (
-score
pe
)
- set the r parameter to 0.62 (
-peR
)
- set the pseudocount paramter to 10 (
-peP
)
- GZIP the output (
-oz
)
cmdline.sh generatescores -p
data/purifications/gavin_raw.txt -score pe -peR 0.62 -peP 10 -c 5.0 -o
PEs.net.gz -oz