# Reference

## All functions
`artmsAnalysisQuantifications()` | Analysis of the Relative Quantifications
`artmsAnnotateSpecie()` | Adding a column with the species name
`artmsAnnotationUniprot()` | Annotate table with Gene Symbol and Name based on Uniprot ID(s)
`artmsAvgIntensityRT()` | Summarize average intensity and retention time per protein
`artmsChangeColumnName()` | Change a specific column name in a given data.frame
`artmsConvertMetabolomics()` | Convert Markview Metabolomics file (alignment table) into a artMS compatible format
`artmsDataPlots()` | Individual Normalized abundance dot plots for every protein
`artmsEnrichLog2fc()` | Enrichment of changes in protein abundance or PTMs
`artmsEnrichProfiler()` | Enrichment analysis using GprofileR
`artmsEvidenceToSAINTq()` | MaxQuant evidence file to SAINTq format
`artmsEvidenceToSaintExpress()` | MaxQuant evidence file to SAINTexpress format
`artmsFilterEvidenceContaminants()` | Remove contaminants and empty proteins from the MaxQuant evidence file
`artmsGeneratePhSiteExtended()` | Generate ph-site specific detailed file
`artmsIsEvidenceNewVersion()` | Check if a given evidencee file was generated by a new version of MaxQuant (v>1)
`artmsIsSpeciesSupported()` | Check if a species is supported and available
`artmsLeaveOnlyUniprotEntryID()` | Leave only the Entry ID from a typical full Uniprot IDs in a given column
`artmsMapUniprot2Entrez()` | Map GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot IDS
`artmsMergeEvidenceAndKeys()` | Merge evidence.txt (or summary.txt) with keys.txt files
`artmsMsstatsSummary()` | Summarize the MSStats results and data quantification
`artmsPhosfateOutput()` | Generate Phosfate Input file
`artmsPhotonOutput()` | Generate PHOTON Input file
`artmsPlotHeatmapQuant()` | Outputs a heatmap of the MSStats results created using the log2fold changes
`artmsProtein2SiteConversion()` | Converts the Protein ID column of the evidence file selected by the user to mod-site-specific notation: `ProteinID` to `ProteinID_AAnumber` notation
`artmsQualityControlEvidenceBasic()` | Quality Control analysis of the MaxQuant evidence file
`artmsQualityControlEvidenceExtended()` | Extended Quality Control of the MaxQuant evidence.txt file
`artmsQualityControlMetabolomics()` | Quality Control analysis of the evidence-like metabolomics dataset
`artmsQualityControlSummaryExtended()` | Quality Control of the MaxQuant summary.txt file
`artmsQuantification()` | Relative quantification using MSstats
`artmsResultsWide()` | Reshape the MSstats results file from long to wide format
`artmsSILACtoLong()` | Convert the SILAC evidence file to MSstats format
`artmsSpectralCounts()` | Outputs the spectral counts from the MaxQuant evidence file.
`artmsVolcanoPlot()` | Volcano plot (log2fc / pvalues)
`artmsWriteConfigYamlFile()` | Write out a template file of the artMS configuration file (yaml)
`artms_config` | artMS configuration template
`artms_data_corum_mito_database` | CORUM Protein Complexes database use for complex enrichment analysis
`artms_data_pathogen_LPN` | LPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDS
`artms_data_pathogen_TB` | TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS
`artms_data_ph_config` | artMS configuration for the available PH dataset
`artms_data_ph_contrast` | Contrast example for the PH dataset
`artms_data_ph_evidence` | Evidence file example
`artms_data_ph_keys` | Keys File Example
`artms_data_ph_msstats_modelqc` | MSstats modelQC example
`artms_data_ph_msstats_results` | MSstats results example
`artms_data_randomDF` | Random data set