# Quality Control of the MaxQuant summary.txt file

Source: `R/qualityControlSummaryExtended.R`
`artmsQualityControlSummaryExtended.Rd`

Performs quality control based on the information available in the MaxQuant summary.txt file.

    artmsQualityControlSummaryExtended(
      summary_file,
      keys_file,
      output_dir = "qc_summary",
      output_name = "qcExtended_summary",
      isFractions = FALSE,
      plotMS1SCANS = TRUE,
      plotMS2 = TRUE,
      plotMSMS = TRUE,
      plotISOTOPE = TRUE,
      printPDF = TRUE,
      verbose = TRUE
    )

## Arguments

summary_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
output_dir | (char) Name for the folder to output the results plots. Default is "qc_summary".
output_name | (char) prefix output name (no extension). Default: "qcExtended_summary"
isFractions | (logical) `TRUE` if it is a 2D experiment (fractions). Default: `FALSE`
plotMS1SCANS | (logical) `TRUE` generates MS1 scan counts plot: Page 1 shows the number of MS1 scans in each BioReplicate. If replicates are present, Page 2 shows the mean number of MS1 scans per condition with error bar showing the standard error of the mean. If isFractions `TRUE`, each fraction is a stack on the individual bar graphs.
plotMS2 | (logical) `TRUE` generates MS2 scan counts plot: Page 1 shows the number of MSs scans in each BioReplicate. If replicates are present, Page 2 shows the mean number of MS1 scans per condition with error bar showing the standard error of the mean. If isFractions `TRUE`, each fraction is a stack on the individual bar graphs.
plotMSMS | (logical) `TRUE` generates MS2 identification rate (%) plot: Page 1 shows the fraction of MS2 scans confidently identified in each BioReplicate. If replicates are present, Page 2 shows the mean rate of MS2 scans confidently identified per condition with error bar showing the standard error of the mean. If isFractions `TRUE`, each fraction is a stack on the individual bar graphs.
plotISOTOPE | (logical) `TRUE` generates Isotope Pattern counts plot: Page 1 shows the number of Isotope Patterns with charge greater than 1 in each BioReplicate. If replicates are present, Page 2 shows the mean number of Isotope Patterns with charge greater than 1 per condition with error bar showing the standard error of the mean. If isFractions `TRUE`, each fraction is a stack on the individual bar graphs.
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

A number of plots from the summary file

## Examples

    # Testing warning if files are not submitted
    test <- artmsQualityControlSummaryExtended(summary_file = NULL,
    keys_file = NULL)
    #> ---------------------------------------------#> artMS: EXTENDED QUALITY CONTROL (-summary.txt based)#> ---------------------------------------------