Parameter options

Calling signature:

gptwosample [-h] [-o DIR] [-t] [-c N] [-p] [-v] [--version] [--backend [PDF,...]]  FILE FILE

where:

FILE                  treatment/control files to compare against each other
-h, --help            show this help message and exit
-o DIR, --out DIR     set output dir [default: ./twosample_out/]
-t, --timeshift       account for timeshifts in data [default: False]
-c N, --confounder N  account for N confounders in data [default: 0]
-p, --plot            plot data into outdir/plots? [default: False]
-v, --verbose         set verbosity level [default: 0]
--version             show program's version number and exit
--backend [PDF,...]   matplotlib backend - see matplotlib.use(backend)

Data format

The format of the two .csv files (FILE FILE in usage) is as follows:

arbitrary x1 ... xl
Gene ID 1 y1 replicate 1 ... yl replicate 1
... ... ... ...
Gene ID 1 y1 replicate k1 ... yl replicate k1
...      
Gene ID n y1 replicate 1 ... yl replicate 1
... ... ... ...
Gene ID n y1 replicate kn ... yl replicate kn

See gptwosample/examples/ToyCondition{1,2].csv for example data files. All values, which cannot be translated by float() will be treated as missing values in the model.

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Accounting for confounding factors