sm.engine.msm_basic package

Submodules

sm.engine.msm_basic.formula_imager module

Functions for creating isotope images from a mass spectrometry dataset

sm.engine.msm_basic.formula_imager.compute_sf_images(sf_peak_imgs)

Group isotope images for the same formula

Returns:

: pyspark.rdd.RDD

RDD of sum formula, list[sparse matrix of intensities]

sm.engine.msm_basic.formula_imager.compute_sf_peak_images(ds, sf_sp_intens)

Combine all pixel intensities for the same formula into isotope images represented as sparse matrices

Returns:

: pyspark.rdd.RDD

RDD of sum formula, (local peak id, sparse matrix of intensities)

sm.engine.msm_basic.formula_imager.sample_spectra(sc, ds, formulas)

Find formulas for which non-zero intensities in some spectra exist

Returns:

: pyspark.rdd.RDD

RDD of (sum formula index, peak local index), (spectrum id, intensity)

sm.engine.msm_basic.formula_imager_segm module

sm.engine.msm_basic.formula_imager_segm.compute_sf_images(sc, ds, sf_peak_df, ppm)

Compute isotopic images for all formula

Returns:

: pyspark.rdd.RDD

RDD of sum formula, list[sparse matrix of intensities]

sm.engine.msm_basic.formula_imager_segm.find_mz_segments(spectra, sf_peak_df, ppm)

sm.engine.msm_basic.formula_imager_segm.gen_iso_peak_images(sc, ds, sf_peak_df, segm_spectra, peaks_per_sp_segm, ppm)

sm.engine.msm_basic.formula_imager_segm.gen_iso_sf_images(iso_peak_images, shape)

sm.engine.msm_basic.formula_img_validator module

Classes and functions for isotope image validation

class sm.engine.msm_basic.formula_img_validator.ImgMeasures(chaos, image_corr, pattern_match)

Bases: object

Container for isotope image metrics

to_tuple(replace_nan=True)

Convert metrics to a tuple

sm.engine.msm_basic.formula_img_validator.get_compute_img_metrics(sample_area_mask, empty_matrix, img_gen_conf)

Returns a function for computing isotope image metrics

sm.engine.msm_basic.formula_img_validator.sf_image_metrics(sf_images, sc, formulas, ds, ds_config)

Compute isotope image metrics for each formula

sm.engine.msm_basic.formula_img_validator.sf_image_metrics_est_fdr(sf_metrics_df, formulas, fdr)

sm.engine.msm_basic.msm_basic_search module

class sm.engine.msm_basic.msm_basic_search.MSMBasicSearch(sc, ds, formulas, fdr, ds_config)

Bases: sm.engine.search_algorithm.SearchAlgorithm

calc_metrics(sf_images)

estimate_fdr(all_sf_metrics_df)

filter_sf_metrics(sf_metrics_df)

search()

Module contents