Files in Viant-Metabolomics/msPurity
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/all-generics.R
R/averaging.R
R/combineAnnotations.R
R/create-database.R
R/createDatabase.R
R/flag-filter-remove.R
R/iw-norm.R
R/matching-algs.R
R/meta_extract.R
R/msPurity.R
R/pcalc.R
R/purityA-0-class.R
R/purityA-av-spectra.R
R/purityA-constructor.R
R/purityA-create-msp.R
R/purityA-filter-frag-spectra.R
R/purityA-frag4feature.R
R/purityA-validate.R
R/purityD-av-spectra.R
R/purityD-class.R
R/purityD-constructor.R
R/purityD-dims-purity.R
R/purityD-fileList.R
R/purityD-filterp.R
R/purityD-subtract.R
R/purityD-writeOut.R
R/purityX-class.R
R/purityX-constructor.R
R/spectral-matching.R
R/spectralMatching.R
R/splinepurity.R
README.rst
inst/CITATION
inst/extdata/iwqe5.rds
inst/extdata/tests/db/createDatabase_example.sqlite
inst/extdata/tests/db/createDatabase_example_OLD.sqlite
inst/extdata/tests/db/create_database_example.sqlite
inst/extdata/tests/db/metab_compound_subset.sqlite
inst/extdata/tests/external_annotations/beams.tsv
inst/extdata/tests/external_annotations/combined.tsv
inst/extdata/tests/external_annotations/metfrag.tsv
inst/extdata/tests/external_annotations/probmetab.tsv
inst/extdata/tests/external_annotations/sirus_csifingerid.tsv
inst/extdata/tests/msp/all.msp
inst/extdata/tests/msp/all_OLD.msp
inst/extdata/tests/msp/av_all.msp
inst/extdata/tests/msp/av_all_OLD.msp
inst/extdata/tests/msp/av_all_dupmeta.msp
inst/extdata/tests/msp/av_all_dupmeta_OLD.msp
inst/extdata/tests/msp/av_all_include_adducts.msp
inst/extdata/tests/msp/av_inter.msp
inst/extdata/tests/msp/av_inter_OLD.msp
inst/extdata/tests/msp/av_intra.msp
inst/extdata/tests/msp/av_intra_OLD.msp
inst/extdata/tests/msp/max.msp
inst/extdata/tests/msp/max_OLD.msp
inst/extdata/tests/msp/recrdt.msp
inst/extdata/tests/msp/recrdt_OLD.msp
inst/extdata/tests/purityA/10_input_filterflagremove.rds
inst/extdata/tests/purityA/1_purityA_pa.rds
inst/extdata/tests/purityA/1_purityA_pa_OLD.rds
inst/extdata/tests/purityA/2_frag4feature_pa.rds
inst/extdata/tests/purityA/2_frag4feature_pa_OLD.rds
inst/extdata/tests/purityA/3_filterFragSpectra_pa.rds
inst/extdata/tests/purityA/3_filterFragSpectra_pa_OLD.rds
inst/extdata/tests/purityA/4_averageIntraFragSpectra_no_filter_pa.rds
inst/extdata/tests/purityA/4_averageIntraFragSpectra_no_filter_pa_OLD.rds
inst/extdata/tests/purityA/5_averageInterFragSpectra_no_filter_pa.rds
inst/extdata/tests/purityA/5_averageInterFragSpectra_no_filter_pa_OLD.rds
inst/extdata/tests/purityA/6_averageAllFragSpectra_no_filter_pa.rds
inst/extdata/tests/purityA/6_averageAllFragSpectra_no_filter_pa_OLD.rds
inst/extdata/tests/purityA/7_averageIntraFragSpectra_with_filter_pa.rds
inst/extdata/tests/purityA/7_averageIntraFragSpectra_with_filter_pa_OLD.rds
inst/extdata/tests/purityA/8_averageInterFragSpectra_with_filter_pa.rds
inst/extdata/tests/purityA/8_averageInterFragSpectra_with_filter_pa_OLD.rds
inst/extdata/tests/purityA/9_averageAllFragSpectra_with_filter_pa.rds
inst/extdata/tests/purityA/9_averageAllFragSpectra_with_filter_pa_OLD.rds
inst/extdata/tests/purityX/1_purityX_grouped_px.rds
inst/extdata/tests/purityX/1_purityX_single_px.rds
inst/extdata/tests/sm/spectralMatching_result.sqlite
inst/extdata/tests/sm/spectralMatching_result_OLD.sqlite
inst/extdata/tests/sm/spectral_matching_result.sqlite
inst/extdata/tests/xcms/ms_only_xcmsnexp.rds
inst/extdata/tests/xcms/ms_only_xset_OLD.rds
inst/extdata/tests/xcms/msms_only_xcmsnexp.rds
inst/extdata/tests/xcms/msms_only_xset.rds
inst/extdata/tests/xcms/msms_only_xset_OLD.rds
man/Getfiles.Rd
man/assessPuritySingle.Rd
man/averageAllFragSpectra-purityA-method.Rd
man/averageInterFragSpectra-purityA-method.Rd
man/averageIntraFragSpectra-purityA-method.Rd
man/averageSpectra-purityD-method.Rd
man/averageSpectraSingle.Rd
man/combineAnnotations.Rd
man/createDatabase.Rd
man/createMSP-purityA-method.Rd
man/create_database.Rd
man/dimsPredictPurity-purityD-method.Rd
man/dimsPredictPuritySingle.Rd
man/filterFragSpectra-purityA-method.Rd
man/filterp-purityD-method.Rd
man/flag_remove.Rd
man/frag4feature-purityA-method.Rd
man/getP-purityD-method.Rd
man/get_additional_mzml_meta.Rd
man/groupPeaks-purityD-method.Rd
man/groupPeaksEx.Rd
man/initialize-purityD-method.Rd
man/iwNormGauss.Rd
man/iwNormQE.5.Rd
man/iwNormRcosine.Rd
man/msPurity.Rd
man/pcalc.Rd
man/purityA.Rd
man/purityD-class.Rd
man/purityX.Rd
man/show-purityA-method.Rd
man/show-purityD-method.Rd
man/show-purityX-method.Rd
man/spectralMatching.Rd
man/spectral_matching.Rd
man/subtract-purityD-method.Rd
man/subtractMZ.Rd
man/validate-purityA-method.Rd
man/writeOut-purityD-method.Rd
msPurity.Rproj
tests/testthat.R
tests/testthat/test.1_pcalc.R
tests/testthat/test.2_purityA.R
tests/testthat/test.2_purityA_OLD.R
tests/testthat/test.3_flagremove.R
tests/testthat/test.4_db.R
tests/testthat/test.4_db_OLD.R
tests/testthat/test.5_sm.R
tests/testthat/test.5_sm_OLD.R
tests/testthat/test.6_combineAnnotations.R
tests/testthat/test.7_purityX.R
tests/testthat/test.8_dims.R
vignettes/figure1_analytical_chemistry.jpg
vignettes/figure2_analytical_chemistry.jpg
vignettes/figure3_analytical_chemistry.jpg
vignettes/isolation.png
vignettes/isolation_exp.png
vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.R
vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd
vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.md
vignettes/msPurity-spectral-database-vignette.R
vignettes/msPurity-spectral-database-vignette.Rmd
vignettes/msPurity-spectral-database-vignette.html
vignettes/msPurity-spectral-database-vignette.md
vignettes/msPurity-vignette.R
vignettes/msPurity-vignette.Rmd
vignettes/msPurity-vignette.html
vignettes/msPurity.Rproj
vignettes/mspurity.bib
vignettes/spectral-database-schema.html
