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)
#> ---------------------------------------------