Analytical R tools for Mass Spectrometry

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Documentation for package ‘artMS’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
artmsEvidenceToSaintExpress	MaxQuant evidence file to SAINTexpress format
artmsEvidenceToSAINTq	MaxQuant evidence file to SAINTq 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