Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (see < http://www.maxquant.org>).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
This package allows users of MaxQuant to generate quality control reports in Html/PDF format.
**Latest: **
See NEWS file for a version history.
drag'n'drop
your txt output folder
onto a batch file
)
Besides this documentation on GitHub, the package vignettes of PTXQC will give you valuable information. After the package is installed (see below), you can browse the vignettes using either of these commands within R:
help(package="PTXQC")
browseVignettes(package = 'PTXQC')
If you do not want to wait that long, have a look at the 'vignettes' subfolder. The top part contains a small table with technical gibberish, but the rest is identical to the vignettes you would see in R.
You will find documentation on
If you want to generate QC reports without actually getting involved in R:
We offer a Batch-file based Drag'n'drop mechanism to trigger PTXQC on any MaxQuant output folder. This only works for Windows (not Linux or MacOS) at the moment -- but you have a Windows anyway to run MaxQuant, right?! See drag'n'drop for details. It takes 10 minutes and you are done!
If you just want the package to use (and maybe even modify) it:
First, install pandoc (see bottom of linked page). Pandoc is required in order to locally build the package vignettes (documentation), but you can also read the vignettes online from the PTXQC GitHub page. More importantly, Pandoc enables PTXQC to write QC reports in HTML format (which come with a help text for each plot and are interactive). PDF reports only contain plots! The reports are printed as PDF by default and additionally as HTML if Pandoc is found. If you install Pandoc later while your R session is already open, you need to close and re-open R in order to make R aware of Pandoc!
You can grab PTXQC from either CRAN or GitHub. GitHub installation will give you the latest package; the CRAN version might be a little older, but is faster to install. Check the NEWS file for CRAN submissions and version.
If an error should occur, this allows to track it down more easily. See FAQ - Installation how to resolve them.
## CRAN
install.packages("PTXQC")
or
## GitHub
if (!require(devtools, quietly = TRUE)) install.packages("devtools")
library("devtools") ## this might give a warning like 'WARNING: Rtools is required ...'. Ignore it.
## use build_vignettes = FALSE if you did not install pandoc or if you encounter errors when building vignettes (e.g. PRIDE ftp unavailable)!
install_github("cbielow/PTXQC", build_vignettes = TRUE, dependencies = TRUE)
To get started, see the help and/or vignettes:
help(package="PTXQC")
browseVignettes(package = 'PTXQC')
Please feel free to report bugs (see below), or issue pull requests!
An overview chart at the beginning of the report will give you a first impression.
Detailed plots can be found in the remainder of each report.
For example input data and full reports, see the 'inst/examples' subfolder.
If you encounter a bug, e.g. error message, wrong figures, missing axis annotation or anything which looks suspicious, please use the GitHub issue tracker and file a report.
You should include
help(package="PTXQC")
within RPlease be as precise as possible when providing the bug report - just imagine what kind of information you would like to have in order to track down the issue. In certain situations, the whole txt-folder or a single MaxQuant file might be helpful to solve the problem.
If you want to see a new metric, or have ideas how to improve the existing ones, just open an issue ticket and leave a description.
PTXQC is published at JPR:
Proteomics Quality Control: Quality Control Software for MaxQuant Results Chris Bielow, Guido Mastrobuoni, and Stefan Kempa J. Proteome Res., 2016, 15 (3), pp 777–787. DOI: 10.1021/acs.jproteome.5b00780
Use PTXQC v0.69.3 if you want the version which was used in the paper, i.e.
use install_github(..., ref="v0.69.3")
when following the Installation procedure.
The input data is available in the 'inst/examples' subfolder.
We recommend to use the most recent PTXQC for the best user experience.
This NEWS file mainly serves as a changelog file, i.e. a list of new features / bugfixes by version number.
Versions uploaded to CRAN are marked with [CRAN].
################################# ######### CHANGELOG ########## #################################
[CRAN] v0.92.0 -- 2017/10/12
[CRAN] v0.91.0 -- 2017/10/06
[CRAN] v0.90.0 -- 2017/08/03
[CRAN] v0.82.6 -- 2017/06/09
[CRAN] v0.82.5 -- 2017/05/04
v0.82.4 -- 2017/04/24
[CRAN] v0.82.3 -- 2017/04/03
[CRAN] v0.82.2 -- 2017/02/18
v0.82.1 -- 2016/11/03
v0.82.0 -- 2016/11/01
v0.81.0 -- 2016/10/18
[CRAN] v0.80.14 -- 2016/10/13
[CRAN] v0.80.13 -- 2016/10/07
v0.80.12 -- 2016/09/28
v0.80.11 -- 2016/08/11
v0.80.10 -- 2016/08/04
v0.80.9 -- 2016/08/02
v0.80.8 -- 2016/07/13
v0.80.7 -- 2016/06/09
v0.80.6 -- 2016/06/06
v0.80.5 -- 2016/04/15
v0.80.4 -- 2016/04/11
v0.80.3 -- 2016/04/08
v0.80.2 -- 2016/04/04
v0.80.1 -- 2016/03/15
v0.80.0 -- 2016/02
v0.70.3
v0.70.2
v0.70.1
v0.70.0