runSECexplorer: Run CCprofiler from SECexplorer y providing ids and their...

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

Description

Run CCprofiler from SECexplorer y providing ids and their type.

Usage

runSECexplorer(ids, type)

Arguments

ids	A character vector containing names or identifiers.
type	A character string specifying the type of ids.

Value

A list containing the following elements:

• conversionRes A list of the following:

  • not_defined A character vector containing all input ids that are not defined in the current version of the package.

  • no_ms_signal A chaacter vector of all input ids that do not have an MS signal in the current SEC experiment.

  • protein_ids A chaacter vector of all uniprotkb accession ids used for further analysis.

  • mapping_table A data.table containing the following information:

    • UNIPROTKB Uniprotkb accession ids.

    • name The combined name for the uniprotkb accession ids. This is UNIPROTKB | uniprot name.

    • input type If the input type was not UNIPROTKB this contains the ids of the input type.

• featureRes A list of 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.