Man pages for MoseleyBioinformaticsLab/FTMS.peakCharacterization
Functionality for Detecting and Characterizing Peaks
| add_peak_list | ZipMS - add_peak_list |
| add_to_zip | add to zip file |
| anova_matrix_test | anova matrix |
| anova_test | anova test |
| area_sum_points | area sum |
| basic_peak_center_intensity | basic peak center |
| bootstrap_samples | generate bootstrap samples |
| calc_point_slopes | calculate subsequent slopes |
| calculate_density | peak density |
| calculate_rsd | rsd calculation |
| CharacterizeMSPeaks | analyze ftms mass-spec data |
| characterize_peaks | characterize peaks from points and picked peaks |
| check_for_zip | check for zip |
| check_frequency_r2 | check r2 |
| check_zip_file | check zip file |
| choose_peak_points_area | choose the peak |
| choose_peak_rsq | choose peak rsq |
| cleanup | ZipMS - cleanup |
| 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 |
| count_raw_peaks | count raw peaks |
| 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 |
| default_scan_filter | default filter |
| define_peak_type | define peak type |
| 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 |
| every_scan_frequency | get frequencies for all data |
| exponential_fit | exponential fit |
| exponential_predict | exponential predictions |
| extract | extract parts of a value |
| extract_raw_method | extract raw method |
| find_peaks | find the peaks |
| find_peaks_diff | find peaks |
| find_signal_regions | find signal |
| frequency_points_to_frequency_regions | frequency points to frequency_regions |
| get_area_peak | get area peak |
| get_area_peak_rejslope | get area peak |
| get_cauchy_peak_info | generate peak info using a cauchy fit |
| get_fitted_peak_info | parabolic fitted peak |
| get_ms_info | get MS info |
| get_mzml_header | extract mzML header |
| get_mzml_metadata | get mzML metadata |
| get_peak_info | get peak info |
| get_raw_ms_metadata | get raw ms metadata |
| get_rsq_peak | get rsq peak |
| import_json | import json |
| import_raw_ms | import raw mass spec data |
| import_xcalibur | import Xcalibur 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 |
| linear_fit | linear fit |
| 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_peaks | generate log intensity |
| 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_points_to_frequency_regions | mz points to frequency regions |
| mz_scans_to_frequency | convert mz to frequency across scans |
| parabolic_fit | parabolic fit |
| peak_info | peak info |
| peak_info2 | peak info2 |
| peak_list_2_json | PeakList to json |
| PeakPickingAnalysis | peak picking analysis |
| pipe | Pipe operator |
| plot_peaks | plot peaks |
| plot_raw_peaks | plot raw peaks |
| plot_tic | plot tic |
| pracma_findpeaks | return peaks |
| predicted_frequency_r2 | calculate r2 |
| raw_metadata_mzml | get raw metadata |
| RawMS | Storing the raw mass spec data and operating on it |
| raw_peak_intensity | raw peaks intensities |
| raw_peaks | raw peaks |
| recalculate_offsets | recalculate offsets |
| r_squared | check fit |
| run_mzml_list | run list of mzML files |
| sample_run_time | determine sample run time |
| save | ZipMS - save |
| scan_mzML | import mzML by scans |
| scan_time_filter | filter scans using time |
| set_internal_map | pick enumerator |
| show_progress | turn progress on off |
| show_temp_dir | ZipMS - show_temp_dir |
| split_region_by_peaks | split signal region |
| ssr | sum of squares residuals |
| system_check | Run a system command and check if it succeeds. |
| test_peak_area | test points area |
| test_peak_area_slope | test points area slope |
| test_peak_rsq | test points |
| tic_normalization | tic normalization |
| transform_residuals | transformed residuals |
| zip_list_contents | list zip file contents |
| zip_ms | make a new ZipMS |
| ZipMS | Represents the zip mass spec file |
