Function reference • ScanCentricPeakCharacterization

All functions

SCCharacterizePeaks: R6 Class Controlling Peak Characterization

SCMzml: R6 Class For mzML Data

SCPeakRegionFinder: R6 Peak Region Finder

SCPeakRegions: Holds all the peak region data

SCZip: Represents the zip mass spec file

ScanCentricPeakCharacterization: ScanCentricPeakCharacterization: A package for direct injection FT-MS data processing.

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_single_frequency_model_default(): 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

.get_scan_polarity(): get_scan_mode

.remove_attrs(): remove attributes

.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_remove_outlier_scans_default(): default outlier 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

mz_scans_to_frequency(): convert mz to frequency across scans

mzml_to_zip(): create initial zip from mzML

parabolic_fit(): parabolic fit

peak_list_2_json(): PeakList to json

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

sc_zip(): make a new SCZip

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