Files in RAMClustR

Mass Spectrometry Metabolomics Feature Clustering and Interpretation

MD5

ChangeLog

README.md

NAMESPACE

DESCRIPTION

R/rc.feature.replace.na.R R/rc.feature.normalize.quantile.R R/rc.feature.normalize.qc.R R/adap.to.rc.R R/import.MSFinder.formulas.R R/manual.annotation.template.R R/rc.cmpd.filter.blanks.R R/annotation.summary.R R/rc.cmpd.get.pathways.R R/import.adap.kdb.R R/write.msp.R R/rc.cmpd.get.classyfire.R R/assign.z.R R/mergeRCobjects.R R/findfeature.R R/getData.R R/get.taxon.cids.R R/rc.feature.normalize.tic.R R/getSmilesInchi.R R/rc.cmpd.replace.na.R R/rc.expand.sample.names.R R/defineExperiment.R R/RCQC.R R/rc.get.csv.data.R R/rc.get.df.data.R R/rc.ramclustr.R R/rc.feature.filter.blanks.R R/rc.get.xmcs.data.R R/rc.restore.qc.samples.R R/rc.remove.qc.R R/rc.cmpd.get.pubchem.R R/change.annotation.R R/impRamSearch.R R/rc.qc.R R/import.msfinder.mssearch.R R/cmpd.summary.R R/export.msfinder.formulas.R R/write.methods.R R/ramclustR.R R/exportDataset.R R/import.sirius.R R/calculate.similarity.R R/rc.feature.filter.cv.R R/rc.cmpd.get.smiles.inchi.R R/rc.cmpd.cv.filter.R R/rc.calibrate.ri.R R/fooddb2msfinder.R R/do.findmain.R R/annotate.R R/rc.feature.normalize.batch.qc.R R/import.MSFinder.structures.R R/rc.export.msp.rc.R R/findmass.R

inst/references.txt

inst/doc/RAMClustR.R

inst/doc/RAMClustR.html

inst/doc/RAMClustR.Rmd

inst/extdata/phenoData_df.rds

inst/extdata/phenoData.csv

inst/extdata/featDefinition.rds

inst/extdata/peaks.csv

inst/extdata/featValues.rds

inst/params/paramsets.Rdata

inst/params/params.csv

inst/params/greek.csv

inst/params/defparamsets.Rdata

build/vignette.rds

tests/testthat.R tests/testthat/test-workflow-comparison.R tests/testthat/test-rc.qc.R tests/testthat/test-rc.feature.normalize.qc.R tests/testthat/test-rc.feature.replace.na.R tests/testthat/test-stepwise-workflow.R tests/testthat/test-rc.feature.normalize.tic.R tests/testthat/test-rc.get.df.data.R tests/testthat/test-do.findmain.R tests/testthat/test-rc.get.csv.data.R tests/testthat/test-rc.feature.filter.cv.R tests/testthat/test-rc.feature.normalize.quantile.R tests/testthat/test-rc.calibrate.ri.R tests/testthat/helper.R tests/testthat/test-rc.ramclustr.R tests/testthat/test-rc.expand.sample.names.R tests/testthat/test-rc.feature.filter.blanks.R tests/testthat/test-rc.feature.normalize.batch.qc.R tests/testthat/test-rc.restore.qc.samples.R tests/testthat/test-rc.remove.qc.R tests/testthat/test-rc.get.xcms.data.R tests/testthat/test.R

tests/testthat/testdata/input.rc.calibrate.ri.rds

tests/testthat/testdata/calibrant.data.csv

tests/testthat/testdata/phenoData_df.rds

tests/testthat/testdata/rc.get.csv.data.rds

tests/testthat/testdata/phenoData.csv

tests/testthat/testdata/rc.expand.sample.names.rds

tests/testthat/testdata/rc.feature.normalize.tic.rds

tests/testthat/testdata/rc.qc.rds

tests/testthat/testdata/rc.get.df.data.rds

tests/testthat/testdata/peaks.csv

tests/testthat/testdata/rc.remove.qc.rds

tests/testthat/testdata/ms1_featureValues.rds

tests/testthat/testdata/rc.feature.replace.na.rds

tests/testthat/testdata/do.findmain.rds

tests/testthat/testdata/test_csv.rds

tests/testthat/testdata/rc.feature.normalize.qc.rds

tests/testthat/testdata/rc.feature.normalize.batch.qc.rds

tests/testthat/testdata/testMetadata.csv

tests/testthat/testdata/rc.feature.normalize.quantile.rds

tests/testthat/testdata/rc.feature.filter.blanks.rds

tests/testthat/testdata/rc.feature.filter.cv.rds

tests/testthat/testdata/test.fillpeaks

tests/testthat/testdata/ms1_featureDefinitions.rds

tests/testthat/testdata/output.msp

tests/testthat/testdata/rc.calibrate.ri.rds

tests/testthat/testdata/rc.restore.qc.samples.rds

tests/testthat/testdata/rc.get.xcms.data.rds

tests/testthat/testdata/clustering/only_rt_rc.ramclustr.rds

tests/testthat/testdata/clustering/normal_rc.ramclustr.rds

vignettes/ExpDes.csv

vignettes/RAMClustR.Rmd

vignettes/spectra/test.mspLib

man/normalized_data_batch_qc.Rd man/check_arguments_filter.blanks.Rd man/rc.get.xcms.data.Rd man/exportDataset.Rd man/assign.z.Rd man/write.msp.Rd man/compute_do.sets.Rd man/rc.get.csv.data.Rd man/rc.cmpd.get.classyfire.Rd man/do.findmain.Rd man/adap.to.rc.Rd man/checks.Rd man/rc.cmpd.get.smiles.inchi.Rd man/rc.get.df.data.Rd man/order_datasets.Rd man/ramclustR.Rd man/filter_blanks.Rd man/cmpd.summary.Rd man/annotate.Rd man/compute_wt_mean.Rd man/rc.remove.qc.Rd man/rc.restore.qc.samples.Rd man/annotation.summary.Rd man/rc.cmpd.filter.cv.Rd man/change.annotation.Rd man/findfeature.Rd man/impRamSearch.Rd man/find_good_features.Rd man/rc.cmpd.filter.blanks.Rd man/rc.feature.normalize.batch.qc.Rd man/rc.feature.replace.na.Rd man/rc.calibrate.ri.Rd man/remove_blanks.Rd man/write.methods.Rd man/get_ExpDes.Rd man/replace_na.Rd man/rc.expand.sample.names.Rd man/create_ramclustObj.Rd man/rc.cmpd.get.pubchem.Rd man/import.msfinder.structures.Rd man/rc.feature.normalize.qc.Rd man/add_params.Rd man/import.msfinder.mssearch.Rd man/getSmilesInchi.Rd man/normalized_data_tic.Rd man/mergeRCobjects.Rd man/write_csv.Rd man/RCQC.Rd man/manual.annotation.template.Rd man/export.msfinder.formulas.Rd man/findmass.Rd man/import.adap.kdb.Rd man/import.sirius.Rd man/define_samples.Rd man/check_arguments_replace.na.Rd man/rc.feature.filter.cv.Rd man/mean_signal_intensities.Rd man/rc.ramclustr.Rd man/getData.Rd man/rc.feature.normalize.tic.Rd man/rc.qc.Rd man/get_instrument_platform.Rd man/rc.feature.normalize.quantile.Rd man/check_arguments_filter.cv.Rd man/rc.export.msp.rc.Rd man/rc.cmpd.replace.na.Rd man/rc.feature.filter.blanks.Rd man/filter_signal.Rd man/compute_SpecAbundAve.Rd man/filter_good_features.Rd man/import.msfinder.formulas.Rd man/get.taxon.cids.Rd man/fooddb2msfinder.Rd man/defineExperiment.Rd

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.