Man pages for USEPA/LUMA
LCMS-Based Untargeted Metabolomics Assistant

AnnotatePeaklistAnnotates Peak.list with In House Library
calc_corrstatCalculate correlation matrices for metabolite groups
calc_cvCalculate coeffient of variation (CV) by pooled QCs
calc_minfracCalculate minimum fraction of features across sample classes
CAMERAFiles_dlgCAMERA Files Dialog Box
CombineFeaturesCombines Features into Metabolites
combine_ion_modesCombines Peak.lists from Two Ionization Modes
CombinePeaklistsCombine Peaklists from different ion modes
combine_phenodataCombine phenotype data in Peak.list
connect_libdbConnects to library database
connect_lumadbConnects to LUMA database
connect_peakdbConnects to peak database
CullBackgroundCulls the Peak.list by Background
CullCVCulls the Peak.list by Percent CV
CullMFCulls the Peak.list by Minimum Fraction
CullVoidVolumeCulls the Peak.list by Void volume
FinalWorkflowConstructor module to finalize LUMA workflow
find_BackgroundFinds background components in Peak.list
FormatForMetaboAnalystRFormatting of metabolite data for MetaboAnalystR.
FormatForSIMCAFormat Peaklists for input into SIMCA
format_MetabolomicDataFormatting of metabolomic data for MetaboAnalystR.
format_simcaFormats Peak.list for SIMCA
gen_filebaseGenerate Filebase
get_featuresRetrieves features from Peak.list in a database
InitWorkflowConstructor module to initiate LUMA Workflow
InputFiles_dlgInput Files Dialog Box
LUMA-packageLCMS Untargeted Metabolomics Assistant
match_AnnotationMatches Peak.list annotations against Annotated Library
mSetObjExample mSetObj
NormalizePeaklistsNormalize Peaklists from different ion modes
normalize_unitnormalize_unit
output_MetaDataPrinting metadata as CSV files for MetaboAnalystR.
ParseCAMERAParses CAMERA annotations
parse_neg_resultsCAMERA Parser in negative mode
parse_pos_resultsCAMERA Parser in positive mode
Peaklist_PosPeaklist_Pos_db Tables
plot_ionduplicateLoop-based EIC Plotter for Ion Mode Duplicates
plot_metgroupLoop-based EIC Plotter for metabolite groups
pre_combine_ion_modesCombines Peak.lists Simply
read_tblReads Peak.list from database
remove_background_peaksRemoves background components from Peak.list
remove_ion_dupRemoves Ion Mode Duplicates
remove_void_volumeRemoves void volume from Peak.list
replace_zeros_normalizeReplaces zeros and normalizes
ScriptInfo_dlgScript Info Dialog Box
search_IonDupSearches Peak.list for ion mode duplicates
SimplyPeaklistsCombine Peaklists simply
sum_featuresSum features by metabolite group
trim_cvTrims by CV
trim_minfracTrims by MinFrac
trim_rtTrims by retention time
wrap_cameraWraps CAMERA
wrap_xcmsWraps xcms
write_tblWrites Peak.list to database
write_xlsxWrites xlsx table
USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.