Parameter options

Calling signature:

gptwosample [-h] [-o DIR] [-t] [-c N] [-p] [-v]
            [--filter FILE] [--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]
--filter FILE only matching genes of each line of FILE will be used for twosampling

–backend [PDF,...] matplotlib backend - see matplotlib.use(backend)

--version show program’s version number and exit

–filter:

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