jinkaido1 / rnaseq_spectral_plsr

RNA-Seq|Hyperspectral Module: Partial least squares regression on transcript expression and hyperspectral data

RNA-Seq & Hyperspectral PLSR

This script (i) splits combined RNA-Seq & hyperspectral data for each transcript into train and test datasets, (ii) runs variable selection to find the lowest MSE, and trained/calibrated using gene expression as response variable and spectral data of selected bands as explanatory variable.

Arguments

• -c, --transcript_csv

  • CSV for a single transcript containing all spectra

• -pod, --plot_out_dir

  • Plot/figure output directory

• -cod, --csv_out_dir

  • CSV output directory (calibration, test, and permutation scores)

• -o, --outdir

  • Main/root output directory

• -m, --model_out_dir

  • PLSR model sav file output directory

• -p, --permutation_out_dir

  • Permutation numpy array output directory

• -t, --test_size

  • Test size for train/test split (default=0.25)

Running the script

To run the scrip, you have to specify at least the CSV:

./rnaseq_spectral_plsr.py -c ./rnaseq_spectra/Gh_A01G026200_tpm_spectra.csv