Man pages for MoseleyBioinformaticsLab/ScanCentricPeakCharacterization
Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner
| add_scan_info | add scan level info |
| add_to_zip | add to zip file |
| area_sum_points | area sum |
| characterize_peaks | characterize peaks from points and picked peaks |
| check_frequency_r2 | check r2 |
| check_ranges_convert_to_regions | frequency points to frequency regions |
| check_zip_file | check zip file |
| choose_frequency_model_builtin | default single model |
| convert_mz_frequency | Convert M/Z to Frequency |
| correct_mean | correct peak mean |
| correct_peak | correct peak sd and mean |
| correct_peak_sd_height | correct peak height and sd |
| correct_variance | correct peak variance |
| create_frequency_regions | create frequency regions |
| create_value | create a value from mantissa and exponent |
| default_correct_offset_function | correct offsets |
| default_offset_predict_function | offset predict function |
| disable_logging | turn logging off |
| dot-get_scan_polarity | get_scan_mode |
| dot-remove_attrs | remove attributes |
| dot-to_data_frame | transform to data frame |
| enable_logging | turn logging on |
| extract | extract parts of a value |
| extract_raw_method | extract raw method |
| filter_scans_builtin | built in filter scan function |
| find_signal_regions | find signal |
| frequency_points_to_frequency_regions | frequency points to frequency_regions |
| get_fitted_peak_info | fitted peak information |
| get_mzml_header | extract mzML header |
| get_mzml_metadata | get mzML metadata |
| get_raw_ms_metadata | get raw ms metadata |
| import_json | import json |
| import_sc_mzml | import mzml mass spec data |
| indicate_standards_contaminents | indicate standards |
| initialize_metadata_from_mzml | initialize metadata from mzML |
| initialize_zip_metadata | initialize metadata |
| integrate_model | integrate model |
| integrate_sides | integrate sides |
| integration_based_area | area from integration |
| json_2_peak_list | PeakList from json |
| json_mzML_2_df | json mzML to data.frame |
| lists_2_json | lists_2_json |
| load_metadata | load metadata |
| loess_to_df | create loess data.frame |
| log_memory | log memory usage |
| log_message | log messages |
| log_with_min | log-transform data |
| meta_export_json | export metadata to json |
| model_peak_center_intensity | model peak center |
| mz_frequency_interpolation | convert mz to frequency using linear fit |
| mzml_to_zip | create initial zip from mzML |
| mz_scans_to_frequency | convert mz to frequency across scans |
| parabolic_fit | parabolic fit |
| peak_list_2_json | PeakList to json |
| pipe | Pipe operator |
| predicted_frequency_r2 | calculate r2 |
| raw_metadata_mzml | get mzml metadata |
| recalculate_offsets | recalculate offsets |
| run_mzml_list | run list of mzML files |
| sample_run_time | determine sample run time |
| ScanCentricPeakCharacterization | ScanCentricPeakCharacterization: A package for direct... |
| SCCharacterizePeaks | R6 Class Controlling Peak Characterization |
| SCMzml | R6 Class For mzML Data |
| SCPeakRegionFinder | R6 Peak Region Finder |
| SCPeakRegions | Holds all the peak region data |
| sc_zip | make a new SCZip |
| SCZip | Represents the zip mass spec file |
| set_internal_map | pick mapping function |
| show_progress | turn progress on off |
| single_pass_normalization | Single Pass Normalization |
| split_region_by_peaks | split signal region |
| ssr | sum of squares residuals |
| transform_residuals | transformed residuals |
| zip_list_contents | list zip file contents |
