Man pages for EMSL-Computing/pspecterlib
PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data
| add_molforms | Add molecular formula objects |
| annotated_spectrum_plot | Annotate a Spectrum with Fragments |
| as.molform | Make a molecular formula object |
| calculate_iso_profile | Calculate an isotope profile |
| collapse_molform | Collapse a molform object to a simple molecular formula |
| convert_proforma | Convert a proforma string to a PTM object |
| count_ion_annotations | Generates a Summary Table of the Number of Ions per Residue |
| coverage_bar_plot | Generates a bar plot of identified residues for a specific... |
| coverage_lit_seq_plot | Displays the literature sequence with identified residues for... |
| coverage_plot | Generate a plot of peptide coverage for a specific protein |
| error_heatmap_plot | Generate a Heatmap of PPM Errors per Ion Type per Residue |
| get_aa_molform | Calculate a molecular formula for an amino acid sequence |
| get_matched_peaks | Matches Calculated Fragments to the Experimental Spectrum and... |
| get_monoisotopic | Get monoisotopic mass from the molecular formula |
| get_ms1ft | Generates the "ms1ft" object, which is Top-Down MS1 Feature... |
| get_mw | Get average mass from the molecular formula |
| get_peak_data | Extracts peak data from a raw or mzML file |
| get_peptide_coverage | Creates the "Peptide Coverage" Object |
| get_protein_table | Counts the Proteins in ScanMetadata and generate "Protein... |
| get_scan_metadata | Creates the "Scan Metadata" object from an MS file |
| get_xic | Get the Extracted Ion Chromatogram object "xic" |
| ion_bar_plot | Make a bar plot of fragments per ion |
| is_sequence | Ensures a string is an acceptable amino acid sequence |
| make_mass_modified_ion | Creates a modified_ion object for get_matched_peaks |
| make_peak_data | Create a peak_data object from an M/Z and Intensity vector |
| ms1_plots | Make the Previous and Next MS1 Plots |
| multiple_modifications | A function to generate a list of properly formatted proforma... |
| multiply_molforms | Multiply molecular formula objects |
| pipe | Pipe operator |
| promex_feature_plot | Generate a feature map from MS1FT data |
| scan_metadata_plot | Make a Scatter Plot of Scan Metadata |
| sequence_plot | Plot the Sequence with Matched Fragments Annotations, split... |
| xic_plot | Make an Extracted Ion Chromatogram |
