# Quality Control analysis of the MaxQuant evidence file

Source: `R/qualityControlEvidenceBasic.R`
`artmsQualityControlEvidenceBasic.Rd`

Quality Control analysis of the MaxQuant evidence file

    artmsQualityControlEvidenceBasic(
      evidence_file,
      keys_file,
      prot_exp = c("AB", "PH", "UB", "AC", "APMS", "PTM:XXX:yy"),
      output_dir = "qc_basic",
      output_name = "qcBasic_evidence",
      isSILAC = FALSE,
      plotINTDIST = FALSE,
      plotREPRO = FALSE,
      plotCORMAT = TRUE,
      plotINTMISC = TRUE,
      plotPTMSTATS = TRUE,
      printPDF = TRUE,
      verbose = TRUE
    )

## Arguments

evidence_file | (char or data.frame) The evidence file path and name, or data.frame
keys_file | (char or data.frame) The keys file path and name or data.frame
prot_exp | (char) Proteomics experiment. 6 options available: `APMS`: affinity purification mass spectrometry `AB`: protein abundance `PH`: protein phosphorylation `UB`: protein ubiquitination (aka ubiquitylation) `AC`: protein acetylation `PTM:XXX:yy` : User defined PTM. Replace XXX with 1 or more 1-letter amino acid codes on which to find modifications (all uppercase). Replace yy with modification name used within the evidence file (require lowercase characters). Example for phosphorylation: `PTM:STY:ph` will find modifications on aa S,T,Y with this example format `_AAGGAPS(ph)PPPPVR_`. This means that the user could select phosphorylation as `PH` or `PTM:STY:ph`
output_dir | (char) Name for the folder to output the results plots. Default is "qc_basic".
output_name | (char) prefix output name (no extension). Default: "qcBasic_evidence"
isSILAC | if `TRUE` processes SILAC input files. Default is `FALSE`
plotINTDIST | if `TRUE` plots both Box-dot plot and Jitter plot of biological replicates based on MS (raw) intensity values, otherwise `FALSE` (default)
plotREPRO | if `TRUE` plots a correlation dotplot for all the combinations of biological replicates of conditions, based on MS Intensity values using features (peptide+charge). Otherwise `FALSE` (default)
plotCORMAT | if `TRUE` (default) plots a Correlation matrix for all the biological replicates using MS Intensity values, Clustering matrix of the MS Intensities
plotINTMISC | if `TRUE` (default) plots several pages, including bar plots of Total Sum of Intensities in BioReplicates, Total Sum of Intensities in Conditions, Total Peptide Counts in BioReplicates, Total Peptide Counts in conditions separated by categories: `CON`: contaminants, `PROT` peptides, `REV` reversed sequences used by MaxQuant to estimate the FDR; Box plots of MS Intensity values per biological replicates and conditions; bar plots of total intensity (excluding contaminants) by bioreplicates and conditions; Barplots of total feature counts by bioreplicates and conditions.
plotPTMSTATS | IF `TRUE` (default) plots stats related to the selected modification, including: bar plot of peptide counts and intensities, broken by `PTM/other` categories; bar plots of total sum-up of MS intensity values by other/PTM categories.
printPDF | If `TRUE` (default) prints out the pdfs. Warning: plot objects are not returned due to the large number of them.
verbose | (logical) `TRUE` (default) shows function messages

## Value

Quality control files and plots

## Examples

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

    # But we recommend the following test:
    # 1. Go to a working directory:
    # setwd("/path/to/your/working/directory/")
    # 2. Run the following command to print out all the pdf files
    # artmsQualityControlEvidenceBasic(evidence_file = artms_data_ph_evidence,
    #                                  keys_file = artms_data_ph_keys,
    #                                  prot_exp =  "PH")
    # 3. Check your working directory and you should find pdf files with
    # all the QC plots