artmsQualityControlSummaryExtended: Quality Control of the MaxQuant summary.txt file

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Quality Control of the MaxQuant summary.txt file

Description

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

Usage

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)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.