annotateComplexFeatures: A helper function to extend a list of complex features with...

In CCprofiler/CCprofiler: Complex feature detection using SEC protein chromatograms.

Description

A helper function to extend a list of complex features with additional information.

Usage

annotateComplexFeatures(traces.obj, complexFeatureStoichiometries,
  complex.annotation)

Arguments

traces.obj	An object of type traces.obj.
complexFeatureStoichiometries	An object of type complexFeatureStoichiometries that is a list containing the following: feature data.table containing complex feature candidates in the following format: left_sw The left boundary of the sliding-window feature. right_sw The right boundary of the sliding-window feature. score The intra-sliding-window-feature correlation. n_subunits The number of protein_ids in the sliding-window feature. apax The apex of the selected peak by the peak-picker. left_pp The left boundary of the selected peak by the peak-picker. right_pp The right boundary of the selected peak by the peak-picker. area The area (entire complex) of the selected peak by the peak-picker. id The protein_ids of the feature separated by semi-colons. total_intensity The intensity of all protein_ids of the feature separated by semi-colons. intensity_ratio The intensity ratio of all protein_ids of the feature separated by semi-colons. stoichiometry The rounded intensity_ratio of all protein_ids of the feature separated by semi-colons.
complex.annotation	A data.table that stores the complex name and protein subunits for each complex_id. complex_id complex_name protein_id

Value

An object of type complexFeaturesAnnotated that is a list containing the following:

• feature data.table containing complex feature candidates in the following format:

  • complex_id The complex_id of the query complex.

  • complex_name The complex_name of the query complex.

  • subunits_annotated The subunits (protein_ids) annotated for the complex separated by semi-colons.

  • n_subunits_annotated The number of subunits (protein_ids) annotated for the complex separated by semi-colons.

  • subunits_with_signal The subunits (protein_ids) with an MS/MS signal for the complex separated by semi-colons.

  • n_subunits_with_signal The number of subunits (protein_ids) with an MS/MS signal for the complex separated by semi-colons.

  • subunits_detected The subunits (protein_ids) detceted in the feature for the complex separated by semi-colons.

  • n_subunits_detected The number of subunits (protein_ids) detceted in the feature for the complex separated by semi-colons.

  • completeness The complex completeness as defined by n_subunits_detected divided by n_subunits_annotated.

  • left_sw The left boundary of the sliding-window feature.

  • right_sw The right boundary of the sliding-window feature.

  • sw_score The intra-sliding-window-feature correlation.

  • left_pp The left boundary of the selected peak by the peak-picker.

  • right_pp The right boundary of the selected peak by the peak-picker.

  • apax The apex of the selected peak by the peak-picker.

  • area The area (entire complex) of the selected peak by the peak-picker.

  • total_intensity The intensity of all protein_ids of the feature separated by semi-colons.

  • intensity_ratio The intensity ratio of all protein_ids of the feature separated by semi-colons.

  • stoichiometry_estimated The rounded intensity_ratio of all protein_ids of the feature separated by semi-colons.

  • monomer_mw The monomer molecular weights of all protein_ids of the feature separated by semi-colons.

  • monomer_sec The monomer sec fraction of all protein_ids of the feature separated by semi-colons.

  • complex_mw_estimated The complex molecular weight as expected fro the stoichiometry_estimated.

  • complex_sec_estimated The complex sec fraction as expected fro the stoichiometry_estimated.

  • sec_diff Difference between complex_sec_estimated and apax of the feature.

CCprofiler/CCprofiler documentation built on May 19, 2021, 7:40 p.m.