Mtrevisan at 14:17, 19 February 2018

2018-02-19T14:17:56Z

Mtrevisan: Created page with "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 us..."

2017-10-03T14:29:02Z

Created page with "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 us..."

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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).

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		+	[[Category:SanXoT software package]]

SanXoTSqueezer - Revision history

Mtrevisan at 14:17, 19 February 2018

Mtrevisan: Created page with "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 us..."