# Mass Spectrometry Metabolomics Feature Clustering and Interpretation

## Documentation for package ‘RAMClustR’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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