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 (char or data.frame) The keys file path and name or data.frame (char) Name for the folder to output the results plots. Default is "qc_summary". (char) prefix output name (no extension). Default: "qcExtended_summary" (logical) TRUE if it is a 2D experiment (fractions). Default: FALSE (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. (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. (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. (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. If TRUE (default) prints out the pdfs. Warning: plot objects are not returned due to the large number of them. (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)#> ---------------------------------------------