artMS_vignette.R
In artMS: Analytical R tools for Mass Spectrometry

## ----set-options, echo=FALSE, cache=FALSE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
options(width = 2000)

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library(artMS)

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#  library(artMS)
#  artmsWriteConfigYamlFile(config_file_name = "my_config.yaml")

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#  artmsQualityControlEvidenceBasic(
#    evidence_file = artms_data_ph_evidence,
#    keys_file = artms_data_ph_keys,
#    prot_exp = "PH")

## ---- eval=TRUE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
artmsQualityControlEvidenceBasic( 
    evidence_file = artms_data_ph_evidence,
    keys_file = artms_data_ph_keys,
    prot_exp = "PH", 
    plotPTMSTATS = TRUE,
    plotINTDIST = FALSE, plotREPRO = FALSE,
    plotCORMAT = FALSE, plotINTMISC = FALSE,
    printPDF = FALSE, verbose = FALSE)

## ---- eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  artmsQualityControlEvidenceExtended(
#     evidence_file = artms_data_ph_evidence,
#     keys_file = artms_data_ph_keys)

## ---- eval = TRUE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
artmsQualityControlEvidenceExtended(
  evidence_file = artms_data_ph_evidence,
  keys_file = artms_data_ph_keys,
  plotPCA = TRUE,
  plotTYPE = TRUE,
  plotPEPTIDES = TRUE,
  plotPSM = FALSE,
  plotIONS = FALSE,
  plotPEPTOVERLAP = FALSE,
  plotPROTEINS = FALSE,
  plotPROTOVERLAP = FALSE,
  plotPIO = FALSE,
  plotCS = FALSE,
  plotME = FALSE,
  plotMOCD = FALSE,
  plotPEPICV = FALSE,
  plotPEPDETECT = FALSE,
  plotPROTICV = FALSE,
  plotPROTDETECT = FALSE,
  plotIDoverlap = FALSE,
  plotSP = FALSE,
  printPDF = FALSE,
  verbose = FALSE)

## ---- eval = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  artmsQualityControlSummaryExtended(summary_file = "summary.txt",
#                                      keys_file = artms_data_ph_keys)

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#  # This example adds annotations to the evidence file available in
#  # artMS, based on the column 'Proteins'.
#  
#  evidence_anno <- artmsAnnotationUniprot(x = artms_data_ph_evidence,
#                                          columnid = 'Proteins',
#                                          species = 'human')

## ---- eval = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  artms_data_ph_evidence <- artmsChangeColumnName(
#                                 dataset = artms_data_ph_evidence,
#                                 oldname = "Phospho..STY.",
#                                 newname = "PH_STY")

## ---- eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  # The data must be annotated (Protein and Gene columns)
#  data_annotated <- artmsAnnotationUniprot(
#                        x = artms_data_ph_msstats_results,
#                        columnid = "Protein",
#                        species = "human")
#  # And then the enrichment
#  enrich_set <- artmsEnrichLog2fc(
#                     dataset = data_annotated,
#                     species = "human",
#                     background = unique(data_annotated$Gene),
#                     verbose = FALSE)

## ---- eval=FALSE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#  # annotate the MSstats results to get the Gene name
#  data_annotated <- artmsAnnotationUniprot(
#                                       x = artms_data_ph_msstats_results,
#                                       columnid = "Protein",
#                                       species = "human")
#  
#  # Filter the list of genes with a log2fc > 2
#  filtered_data <-
#  unique(data_annotated$Gene[which(data_annotated$log2FC > 2)])
#  
#  # And perform enrichment analysis
#  data_annotated_enrich <- artmsEnrichProfiler(
#                                     x = filtered_data,
#                                     categorySource = c('KEGG'),
#                                     species = "hsapiens",
#                                     background = unique(data_annotated$Gene))