---
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] results.

## Input

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

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, you can rename any .txt file if you want PTXQC to ignore it.

## 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. 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]: http://www.maxquant.org
  [Ref_VignCust]: https://github.com/cbielow/PTXQC/blob/master/vignettes/PTXQC-CustomizeReport.Rmd

