SanXoTSqueezer

SanXoTSqueezer v0.12 is a program made in the Jesus Vazquez Cardiovascular Proteomics Lab at Centro Nacional de Investigaciones Cardiovasculares, used mainly to find, while using the Systems Biology triangle, which categories contain a determined number of proteins that are changing more than an FDR set by the user.

SanXoTSqueezer needs two input files:

• a lower level stats file (command -l)
• a higher (or upper) level stats file (command -u)

And delivers one output file:

• the list of changing higher level elements (which can be used as SanXoTGauss input to depict gaussians of relevant higher level elements).

Usage:

sanxotsqueezer.py -l[lower level stats file] -u[upper level stats file] [OPTIONS]

Arguments:

  -h, --help          Display this help and exit.
  -a, --analysis=string
                      Use a prefix for the output files. If this is not
                      provided, then the prefix will be garnered from the
                      stats file.
  -f, --fdr=float     FDR to filter data. Default is 0.05. If -z is used, then
                      the program will filter only by Z.
  -l, --lowerstats=filename
                      The lower level stats input file.
  -L, --logfile=filename
                      To use a non-default name for the log file.
  -n, --minelements=integer
                      The minimum number of lower level elements that a higher
                      level element must include in the stats file. Default
                      is 2 (the minimum).
  -N, --maxelements=integer
                      The maximum number of lower level elements that a higher
                      level element must include in the stats file. Default
                      is 1e6.
  -o, --outputfile=filename
                      To use a non-default file name for the sigmoid table.
  -p, --place, --folder=foldername
                      To use a different common folder for the output files.
                      If this is not provided, the folder used will be the
                      same as the lower stats file folder.
  -u, --upperstats=filename
                      The higher (upper) level stats input file.
  -z, --sigmas=float  Filter by Z (the number of sigmas the higher level
                      element is deviating from the average). Note that by
                      using this option, you will prevent the program from
                      filtering by FDR (see -f).