PTXQC generates quality control reports for MaxQuant txt data, and OpenMS mzTab data.
When a full report is generated, PTXQC requires the following input files.
MaxQuant:
These files can be found in the <baseDir>/combined/txt
folder after MaxQuant analysis successfully finished.
Here, <baseDir>
is your main MaxQuant project folder containing your Raw files.
OpenMS:
Note: PTX-QC will compute all metrics for which input data is present. MzTab files from other software packages (even mzTab from MaxQuant) will be missing some data and thus only produce a small subset of metrics.
If you are not interested in the full report, PTXQC can be configured to look only at some of these files by editing the YAML file. See the PTX-CustomizeReport vignette
vignette("PTXQC-CustomizeReport", package = "PTXQC")
for details. Alternatively (for .txt input), you can rename any .txt file you want PTXQC to ignore.
By default, PTXQC will generate a report in both Html and PDF format.
To enable/disable a certain format (Html/PDF), just set it in the YAML config file (see above for the vignette hint on report customization).
Further output files (with the same prefix name as the Html/PDF report), include
report_vXXX_heatmap.txt
(values of the overview heatmap)report_vXXX_filename_sort.txt
(customize the order and naming of Raw files in the report)report_v0XXX.yaml
(the configuration file)The YAML configuration file is created the first time you run PTXQC on a txt-folder or mzTab file. Customize it as you see fit.
Read more about report_vXXX_filename_sort.txt
and report_vXXX.yaml
in the PTX-CustomizeReport vignette.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.