Mass Spectrometry Metabolomics Feature Clustering and
Interpretation
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Documentation for package ‘RAMClustR’ version 1.3.1
Help Pages
| adap.to.rc | adap.to.rc |
| add_params | add_params |
| annotate | evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR object |
| annotation.summary | annotation.summary() |
| assign.z | assign.z |
| change.annotation | evaluate ramSearch, MSFinder mssearch, MSFinder Structure, MSFinder Formula, and findmain output to annotate spectra of ramclustR object |
| checks | checks |
| check_arguments_filter.blanks | check_arguments_filter.blanks |
| check_arguments_filter.cv | check_arguments_filter.cv |
| check_arguments_replace.na | check_arguments_replace.na |
| cmpd.summary | cmpd.summary |
| compute_do.sets | compute_do.sets |
| compute_SpecAbundAve | compute_SpecAbundAve |
| compute_wt_mean | compute_wt_mean |
| create_ramclustObj | create_ramclustObj |
| defineExperiment | defineExperiment |
| define_samples | define_samples |
| do.findmain | do.findmain |
| export.msfinder.formulas | export MSFinder formula prediction results in tabular format. |
| exportDataset | exportDataset |
| filter_blanks | filter_blanks |
| filter_good_features | filter_good_features |
| filter_signal | filter_signal |
| findfeature | findfeature |
| findmass | findmass |
| find_good_features | find_good_features |
| fooddb2msfinder | foodb2msfinder |
| get.taxon.cids | get.taxon.cids |
| getData | getData |
| getSmilesInchi | getSmilesInchi |
| get_ExpDes | get_ExpDes |
| get_instrument_platform | get_instrument_platform |
| import.adap.kdb | import.adap.kdb |
| import.msfinder.formulas | import.msfinder.formulas |
| import.msfinder.mssearch | import.MSFinder.mssearch |
| import.msfinder.structures | write.methods |
| import.sirius | import.sirius |
| impRamSearch | impRamSearch |
| manual.annotation.template | manual.annotation.template |
| mean_signal_intensities | mean_signal_intensities |
| mergeRCobjects | mergeRCobjects |
| normalized_data_batch_qc | normalized_data_batch_qc |
| normalized_data_tic | normalized_data_tic |
| order_datasets | order_datasets |
| ramclustR | ramclustR |
| rc.calibrate.ri | rc.calibrate.ri |
| rc.cmpd.filter.blanks | rc.cmpd.filter.blanks |
| rc.cmpd.filter.cv | rc.cmpd.filter.cv |
| rc.cmpd.get.classyfire | getClassyFire |
| rc.cmpd.get.pubchem | rc.cmpd.get.pubchem |
| rc.cmpd.get.smiles.inchi | getSmilesInchi |
| rc.cmpd.replace.na | rc.cmpd.replace.na |
| rc.expand.sample.names | rc.expand.sample.names |
| rc.export.msp.rc | rc.export.msp.rc |
| rc.feature.filter.blanks | rc.feature.filter.blanks |
| rc.feature.filter.cv | rc.feature.filter.cv |
| rc.feature.normalize.batch.qc | rc.feature.normalize.batch.qc |
| rc.feature.normalize.qc | rc.feature.normalize.qc |
| rc.feature.normalize.quantile | rc.feature.normalize.quantile |
| rc.feature.normalize.tic | rc.feature.normalize.tic |
| rc.feature.replace.na | rc.feature.replace.na |
| rc.get.csv.data | rc.get.csv.data |
| rc.get.df.data | rc.get.df.data |
| rc.get.xcms.data | rc.get.xcms.data |
| rc.qc | rc.qc |
| rc.ramclustr | rc.ramclustr |
| rc.remove.qc | rc.remove.qc |
| rc.restore.qc.samples | rc.restore.qc.samples |
| RCQC | RCQC |
| remove_blanks | remove_blanks |
| replace_na | replace_na |
| write.methods | write.methods |
| write.msp | write.msp |
| write_csv | write_csv |