SECexplorer_processing: SECexplorer processing.

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

Description

SECexplorer processing.

Usage

SECexplorer_processing(protein_ids, traces.obj)

Arguments

protein_ids	A character vector containing UNIPROTKB accession ids.
traces.obj	An object of type traces.obj.

Value

A list containing the following:

• traces An object of type traces.obj. Filtered for input ids.

• features 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.