Source code for peptdeep.mass_spec.mass_calibration

from sklearn.neighbors import KNeighborsRegressor
import pandas as pd
import numpy as np



[docs]
def get_fragment_median(start_end_idxes: tuple, frag_df: pd.DataFrame):
    start_idx, end_idx = start_end_idxes
    ret = np.nanmedian(frag_df.values[start_idx:end_idx])
    if np.isnan(ret):
        return 0.0
    else:
        return ret




[docs]
def calibrate_one(start_end_shift, frag_df):
    start_idx, end_idx, mass_shift = start_end_shift
    frag_df.values[int(start_idx) : int(end_idx)] -= mass_shift




[docs]
class MassCalibratorForRT_KNN:
    """Using KNN to calibrate measured m/z across RT."""


[docs]
    def __init__(self, n_neighbors=5):
        self._n_neighbors = n_neighbors
        self.model = KNeighborsRegressor(n_neighbors)



[docs]
    def fit(self, psm_df: pd.DataFrame, mass_error_df: pd.DataFrame):
        mass_error_df = mass_error_df.replace(np.inf, np.nan)
        mean_merrs = (
            psm_df[["frag_start_idx", "frag_stop_idx"]]
            .apply(get_fragment_median, axis=1, frag_df=mass_error_df)
            .values
        )
        self.model.fit(psm_df.rt.values.reshape((-1, 1)), mean_merrs.reshape(-1, 1))



[docs]
    def calibrate(
        self, psm_df: pd.DataFrame, mass_error_df: pd.DataFrame
    ) -> pd.DataFrame:
        psm_df["frag_mass_shift"] = self.model.predict(
            psm_df.rt.values.reshape((-1, 1))
        ).reshape(-1)
        psm_df[["frag_start_idx", "frag_stop_idx", "frag_mass_shift"]].apply(
            calibrate_one, axis=1, frag_df=mass_error_df
        ).values
        return mass_error_df