Files in MoseleyBioinformaticsLab/ScanCentricPeakCharacterization
Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner

.Rbuildignore
.Renviron
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.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md R/PeakPicking.R R/SCCharacterizePeaks.R R/SCMzml.R R/SCPeakRegions.R R/SCZip.R R/SMIRFE_assignments.R R/ScanCentricPeakCharacterization.R R/extract_raw_data.R R/file_metadata.R R/finding_peaks.R R/frequency.R R/indicate_standards.R R/json.R R/logging.R R/mapping.R R/offsets.R R/peak_sd_intensity_corrections.R R/utils-pipe.R R/utils.R R/zip_methods.R
R/zzz.R
README.Rmd
README.html
README.md
_pkgdown.yml
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inst/CITATION
inst/extdata/filtered_multiscan_test.mzML
inst/extdata/lipid_example.json
inst/extdata/lipid_example.mzML
inst/extdata/test_mz.rds
inst/extdata/test_peaks_mz.rds
integration_test/aaecf_emfs.csv
integration_test/run_integration_test.R
integration_test/search_parameters.txt
man/SCCharacterizePeaks.Rd man/SCMzml.Rd man/SCPeakRegionFinder.Rd man/SCPeakRegions.Rd man/SCZip.Rd man/ScanCentricPeakCharacterization.Rd man/add_scan_info.Rd man/add_to_zip.Rd man/area_sum_points.Rd man/characterize_peaks.Rd man/check_frequency_r2.Rd man/check_ranges_convert_to_regions.Rd man/check_zip_file.Rd man/choose_frequency_model_builtin.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/create_frequency_regions.Rd man/create_value.Rd man/default_correct_offset_function.Rd man/default_offset_predict_function.Rd man/disable_logging.Rd man/dot-get_scan_polarity.Rd man/dot-remove_attrs.Rd man/dot-to_data_frame.Rd man/enable_logging.Rd man/extract.Rd man/extract_raw_method.Rd
man/figures/README-change-model-1.png
man/figures/README-check-frequency-1.png
man/figures/README-filter-scans-plot-1.png
man/figures/README-scan-info-plot-1.png
man/figures/README-show_frequency-1.png
man/figures/README-show_predictions-1.png
man/figures/README-show_spacing-1.png
man/filter_scans_builtin.Rd man/find_signal_regions.Rd man/frequency_points_to_frequency_regions.Rd man/get_fitted_peak_info.Rd man/get_mzml_header.Rd man/get_mzml_metadata.Rd man/get_raw_ms_metadata.Rd man/import_json.Rd man/import_sc_mzml.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/lists_2_json.Rd man/load_metadata.Rd man/loess_to_df.Rd man/log_memory.Rd man/log_message.Rd man/log_with_min.Rd man/meta_export_json.Rd man/model_peak_center_intensity.Rd man/mz_frequency_interpolation.Rd man/mz_scans_to_frequency.Rd man/mzml_to_zip.Rd man/parabolic_fit.Rd man/peak_list_2_json.Rd man/pipe.Rd man/predicted_frequency_r2.Rd man/raw_metadata_mzml.Rd man/recalculate_offsets.Rd man/run_mzml_list.Rd man/sample_run_time.Rd man/sc_zip.Rd man/set_internal_map.Rd man/show_progress.Rd man/single_pass_normalization.Rd man/split_region_by_peaks.Rd man/ssr.Rd man/transform_residuals.Rd man/zip_list_contents.Rd
project.Rproj
tests/testthat.R
tests/testthat/test-filtered-scans.R
tests/testthat/test-generators.R tests/testthat/test-import-data.R tests/testthat/test-metadata.R tests/testthat/test-peak-characterization.R
tests/testthat/test-peak-fitting-org_fitted_peaks.rds
tests/testthat/test-peak-fitting.R
vignettes/.gitignore
vignettes/Quick_Start.Rmd vignettes/full-peak-characterization.Rmd
vignettes/scpc.bib
MoseleyBioinformaticsLab/ScanCentricPeakCharacterization documentation built on March 29, 2024, 11:32 p.m.