PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data


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Documentation for package ‘pspecterlib’ version 1.1.0

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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 protein
coverage_lit_seq_plot Displays the literature sequence with identified residues for a specific protein
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 creates the "Matched Peak" object
get_monoisotopic Get monoisotopic mass from the molecular formula
get_ms1ft Generates the "ms1ft" object, which is Top-Down MS1 Feature data
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 Table" object
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 strings
multiply_molforms Multiply molecular formula objects
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 by a,b,c and x,y,z annotations
xic_plot Make an Extracted Ion Chromatogram