Files in MoseleyBioinformaticsLab/FTMS.peakCharacterization

Functionality for Detecting and Characterizing Peaks

LICENSE.md R/CharacterizeMSPeaks.R R/PeakPicking.R R/PeakRegions.R R/RawMS.R R/SMIRFE_assignments.R R/ZipMS.R R/extract_raw_data.R R/file_metadata.R R/finding_peaks.R R/frequency.R R/importdata.R R/indicate_standards.R R/json.R R/logging.R R/offsets.R R/peak_sd_intensity_corrections.R R/sample_normalization.R R/unzip_functions.R R/utils-pipe.R R/utils.R R/viewing_peaks.R R/zip_methods.R R/zzz.R README.Rmd README.md integration_test/run_integration_test.R man/CharacterizeMSPeaks.Rd man/PeakPickingAnalysis.Rd man/RawMS.Rd man/ZipMS.Rd man/add_peak_list.Rd man/add_to_zip.Rd man/anova_matrix_test.Rd man/anova_test.Rd man/area_sum_points.Rd man/basic_peak_center_intensity.Rd man/bootstrap_samples.Rd man/calc_point_slopes.Rd man/calculate_density.Rd man/calculate_rsd.Rd man/characterize_peaks.Rd man/check_for_zip.Rd man/check_frequency_r2.Rd man/check_zip_file.Rd man/choose_peak_points_area.Rd man/choose_peak_rsq.Rd man/cleanup.Rd man/convert_mz_frequency.Rd man/correct_mean.Rd man/correct_peak.Rd man/correct_peak_sd_height.Rd man/correct_variance.Rd man/count_raw_peaks.Rd man/create_frequency_regions.Rd man/create_value.Rd man/default_correct_offset_function.Rd man/default_offset_predict_function.Rd man/default_scan_filter.Rd man/define_peak_type.Rd man/disable_logging.Rd man/dot-get_scan_polarity.Rd man/dot-remove_attrs.Rd man/dot-to_data_frame.Rd man/every_scan_frequency.Rd man/exponential_fit.Rd man/exponential_predict.Rd man/extract.Rd man/extract_raw_method.Rd man/find_peaks.Rd man/find_peaks_diff.Rd man/find_signal_regions.Rd man/frequency_points_to_frequency_regions.Rd man/get_area_peak.Rd man/get_area_peak_rejslope.Rd man/get_cauchy_peak_info.Rd man/get_fitted_peak_info.Rd man/get_ms_info.Rd man/get_mzml_header.Rd man/get_mzml_metadata.Rd man/get_peak_info.Rd man/get_raw_ms_metadata.Rd man/get_rsq_peak.Rd man/import_json.Rd man/import_raw_ms.Rd man/import_xcalibur.Rd man/indicate_standards_contaminents.Rd man/initialize_metadata_from_mzml.Rd man/initialize_zip_metadata.Rd man/integrate_model.Rd man/integrate_sides.Rd man/integration_based_area.Rd man/json_2_peak_list.Rd man/json_mzML_2_df.Rd man/linear_fit.Rd man/lists_2_json.Rd man/load_metadata.Rd man/loess_to_df.Rd man/log_memory.Rd man/log_message.Rd man/log_peaks.Rd man/log_with_min.Rd man/meta_export_json.Rd man/model_peak_center_intensity.Rd man/mz_frequency_interpolation.Rd man/mz_points_to_frequency_regions.Rd man/mz_scans_to_frequency.Rd man/mzml_to_zip.Rd man/parabolic_fit.Rd man/peak_info.Rd man/peak_info2.Rd man/peak_list_2_json.Rd man/pipe.Rd man/plot_peaks.Rd man/plot_raw_peaks.Rd man/plot_tic.Rd man/pracma_findpeaks.Rd man/predicted_frequency_r2.Rd man/r_squared.Rd man/raw_metadata_mzml.Rd man/raw_peak_intensity.Rd man/raw_peaks.Rd man/recalculate_offsets.Rd man/run_mzml_list.Rd man/sample_run_time.Rd man/save.Rd man/scan_mzML.Rd man/scan_time_filter.Rd man/set_internal_map.Rd man/show_progress.Rd man/show_temp_dir.Rd man/split_region_by_peaks.Rd man/ssr.Rd man/system_check.Rd man/test_peak_area.Rd man/test_peak_area_slope.Rd man/test_peak_rsq.Rd man/tic_normalization.Rd man/transform_residuals.Rd man/zip_list_contents.Rd man/zip_ms.Rd tests/testthat.R tests/testthat/test-filtered-scans.R tests/testthat/test-import-data.R tests/testthat/test-metadata.R tests/testthat/test-peak-characterization.R tests/testthat/test-peak_finding.R vignettes/metadata.Rmd vignettes/metadata_alt.Rmd vignettes/mzml_r6_classes.Rmd vignettes/zip_file_testing.Rmd