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:
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.