Example Scripts

Here’s a quick run through of key functionality in DIMEpy.l

import dimepy
import os

data_dir = "/path/to/mzMLs"

sl = dimepy.SpectrumList()

for fn in os.listdir(data_dir):
     # Appending the file name to the data directory
     fp = os.path.join(data_dir,fn)

     # We only have two classes, denoted by the first letter of the file
     strat = fn[0]

     # Note how I'm applying mean-based snr estimation
     spec = dimepy.Spectrum(fp, fn, stratification=strat, snr_estimator="mean")

     # As these are polarity-switching, I'm limiting to positive
     spec.limit_polarity("positive")

     # A threshold of 3 seemed fine from earlier.
     spec.limit_infusion(3)

     # Make sure I load the scans
     spec.load_scans()

     # Appending the Spectrum object to the SL
     sl.append(spec)

sl.detect_outliers(3, verbose=True)

sl.bin(0.25)
sl.value_imputate()
sl.transform()
sl.normalise()

sl.to_csv("/path/to/output.csv", output_type="matrix")