Package: ScanCentricPeakCharacterization 0.3.65

Robert M Flight

ScanCentricPeakCharacterization: Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner

Provides a functions and classes for detecting, characterizing, and integrating peaks in a scan-centric manner from direct-injection mass spectrometry data.

Authors:Robert M Flight [aut, cre]

ScanCentricPeakCharacterization_0.3.65.tar.gz
ScanCentricPeakCharacterization_0.3.65.zip(r-4.5)ScanCentricPeakCharacterization_0.3.65.zip(r-4.4)ScanCentricPeakCharacterization_0.3.65.zip(r-4.3)
ScanCentricPeakCharacterization_0.3.65.tgz(r-4.4-any)ScanCentricPeakCharacterization_0.3.65.tgz(r-4.3-any)
ScanCentricPeakCharacterization_0.3.65.tar.gz(r-4.5-noble)ScanCentricPeakCharacterization_0.3.65.tar.gz(r-4.4-noble)
ScanCentricPeakCharacterization_0.3.65.tgz(r-4.4-emscripten)ScanCentricPeakCharacterization_0.3.65.tgz(r-4.3-emscripten)
ScanCentricPeakCharacterization.pdf |ScanCentricPeakCharacterization.html✨
ScanCentricPeakCharacterization/json (API)
NEWS

# Install 'ScanCentricPeakCharacterization' in R:
install.packages('ScanCentricPeakCharacterization', repos = c('https://moseleybioinformaticslab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/moseleybioinformaticslab/scancentricpeakcharacterization/issues

On CRAN:

62 exports 0.36 score 144 dependencies 1 scripts

Last updated 6 months agofrom:2373d738be (on *release). Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winWARNINGSep 12 2024
R-4.5-linuxWARNINGSep 12 2024
R-4.4-winWARNINGSep 12 2024
R-4.4-macWARNINGSep 12 2024
R-4.3-winWARNINGSep 12 2024
R-4.3-macWARNINGSep 12 2024

Exports:%>%add_scan_infoadd_to_zipcharacterize_peakscheck_frequency_r2check_ranges_convert_to_regionscheck_zip_filechoose_frequency_model_builtinconvert_mz_frequencycorrect_meancorrect_peakcorrect_peak_sd_heightcorrect_variancecreate_frequency_regionsdefault_correct_offset_functiondefault_offset_predict_functiondisable_loggingenable_loggingextract_raw_methodfilter_scans_builtinfind_signal_regionsfrequency_points_to_frequency_regionsget_fitted_peak_infoget_mzml_headerget_mzml_metadataget_raw_ms_metadataimport_sc_mzmlindicate_standards_contaminentsinitialize_metadata_from_mzmlinitialize_zip_metadataintegrate_modeljson_2_peak_listjson_mzML_2_dflists_2_jsonload_metadataloess_to_dflog_memorylog_messagemeta_export_jsonmodel_peak_center_intensitymz_frequency_interpolationmz_scans_to_frequencymzml_to_zippeak_list_2_jsonpredicted_frequency_r2raw_metadata_mzmlrecalculate_offsetsrun_mzml_listsample_run_timesc_zipSCCharacterizePeaksSCMzmlSCPeakRegionFinderSCPeakRegionsSCZipset_internal_mapshow_progresssingle_pass_normalizationsplit_region_by_peaksssrtransform_residualszip_list_contents

Dependencies:abindaffyaffyioAnnotationFilteraskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcellrangercliclueclustercodetoolscolorspacecowplotcpp11crayoncrosstalkcurldata.tabledebugmeDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrknitrProgressBarlabelinglambda.rlaterlatticelazyevallifecyclelimmalubridatemagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpracmapreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadxlrematchreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangetinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryamlzlibbioc

Full Peak Characterization

Robert M Flight

Rendered fromfull-peak-characterization.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2023-04-06
Started: 2023-04-05

Quick Start

Rendered fromQuick_Start.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2022-05-23
Started: 2022-05-23

Readme and manuals

Help Manual

Help pageTopics
get_scan_mode.get_scan_polarity
remove attributes.remove_attrs
transform to data frame.to_data_frame
add scan level infoadd_scan_info
add to zip fileadd_to_zip
area sumarea_sum_points
characterize peaks from points and picked peakscharacterize_peaks
check r2check_frequency_r2
frequency points to frequency regionscheck_ranges_convert_to_regions
check zip filecheck_zip_file
default single modelchoose_frequency_model_builtin
Convert M/Z to Frequencyconvert_mz_frequency
correct peak meancorrect_mean
correct peak sd and meancorrect_peak
correct peak height and sdcorrect_peak_sd_height
correct peak variancecorrect_variance
create frequency regionscreate_frequency_regions
create a value from mantissa and exponentcreate_value
correct offsetsdefault_correct_offset_function
offset predict functiondefault_offset_predict_function
turn logging offdisable_logging
turn logging onenable_logging
extract parts of a valueextract
extract raw methodextract_raw_method
built in filter scan functionfilter_scans_builtin
find signalfind_signal_regions
frequency points to frequency_regionsfrequency_points_to_frequency_regions
fitted peak informationget_fitted_peak_info
extract mzML headerget_mzml_header
get mzML metadataget_mzml_metadata
get raw ms metadataget_raw_ms_metadata
import jsonimport_json
import mzml mass spec dataimport_sc_mzml
indicate standardsindicate_standards_contaminents
initialize metadata from mzMLinitialize_metadata_from_mzml
initialize metadatainitialize_zip_metadata
integrate modelintegrate_model
integrate sidesintegrate_sides
area from integrationintegration_based_area
PeakList from jsonjson_2_peak_list
json mzML to data.framejson_mzML_2_df
lists_2_jsonlists_2_json
load metadataload_metadata
create loess data.frameloess_to_df
log memory usagelog_memory
log messageslog_message
log-transform datalog_with_min
export metadata to jsonmeta_export_json
model peak centermodel_peak_center_intensity
convert mz to frequency using linear fitmz_frequency_interpolation
convert mz to frequency across scansmz_scans_to_frequency
create initial zip from mzMLmzml_to_zip
parabolic fitparabolic_fit
PeakList to jsonpeak_list_2_json
calculate r2predicted_frequency_r2
get mzml metadataraw_metadata_mzml
recalculate offsetsrecalculate_offsets
run list of mzML filesrun_mzml_list
determine sample run timesample_run_time
make a new SCZipsc_zip
ScanCentricPeakCharacterization: A package for direct injection FT-MS data processing.ScanCentricPeakCharacterization
R6 Class Controlling Peak CharacterizationSCCharacterizePeaks
R6 Class For mzML DataSCMzml
R6 Peak Region FinderSCPeakRegionFinder
Holds all the peak region dataSCPeakRegions
Represents the zip mass spec fileSCZip
pick mapping functionset_internal_map
turn progress on offshow_progress
Single Pass Normalizationsingle_pass_normalization
split signal regionsplit_region_by_peaks
sum of squares residualsssr
transformed residualstransform_residuals
list zip file contentszip_list_contents