---
title: "Input/Output data for PTXQC"
author: "Chris Bielow <chris.bielow@fu-berlin.de>"
date: '`r Sys.Date()`'
output:
  html_document: default
  pdf_document: null
vignette: >
  %\VignetteIndexEntry{Input/Output data for PTXQC}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

# Input/Output data for PTXQC

PTXQC generates quality control reports for [MaxQuant] txt data, and [OpenMS] mzTab data.

## Input

When a full report is generated, PTXQC requires the following **input files**.
  
MaxQuant:  

  - parameters.txt
  - summary.txt
  - proteinGroups.txt
  - evidence.txt
  - msms.txt
  - msmsScans.txt
  
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:

  - an .mzTab file from the QualityControl TOPP tool (see [OpenMSdoc] --> TOPP documentation --> QualityControl)
  
  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][Ref_VignCust] vignette
```{r, eval=FALSE}
vignette("PTXQC-CustomizeReport", package = "PTXQC")
```
for details. Alternatively (for .txt input), you can rename any .txt file you want PTXQC to ignore.

## Output

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][Ref_VignCust] vignette.
  

  [MaxQuant]: https://maxquant.org
  [OpenMS]: https://openms.de/
  [OpenMSdoc]: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/index.html
  [Ref_VignCust]: https://github.com/cbielow/PTXQC/blob/master/vignettes/PTXQC-CustomizeReport.Rmd