README.md

artMS

Analytical R Tools for Mass Spectrometry

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Overview

artMS is an R package that provides a set of tools for the analysis and integration of large-scale proteomics (mass-spectrometry-based) datasets obtained using the popular proteomics software package MaxQuant. The functions available in artMS can be grouped into 4 major categories:

artMS performs the different analyses taking as input the following files:

How to install

We assume that you have both R and RStudio already installed on your system. Please, ensure that your system is running an R version >= 3.6 or otherwise nothing will work (Bioconductor requirement). You can check the R version currently running on your system by executing this command in RStudio:

getRversion()

If the outcome is >= 3.6.0, congratulations! you can move forward

If it is not, then you need to install the latest version of R in your system. After updating to the latest R version, open RStudio and try again getRversion() to make sure it worked.

Two options to install artMS

Official BioConductor releases (recommended)

artMS is available on BioConductor. Run the following lines:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("artMS", version = "3.8")

Why Bioconductor? Here you can find a nice summary of good reasons.

Development version from this repo

(Warning: not stable, but it has the latest)

Assuming that you have an R (>= 3.6) version running on your system, follow these steps:

install.packages("devtools")
library(devtools)
install_github("biodavidjm/artMS")

Check that it is up and running by checking, for example, the documentation of the qc function artmsQualityControlEvidenceBasic:

library(artMS)
?artmsQualityControlEvidenceBasic

Once installed, we suggest you to do a quick test by running the quality control functions using the "evidence" (artms_data_ph_evidence) and "keys" (artms_data_ph_keys) files included in artMS as test datasets.

# First go to a local working directory: several pdfs will be generated
# setwd("/path/to/your/working/directory/")

# And run:
artmsQualityControlEvidenceBasic(evidence_file = artms_data_ph_evidence,
                                  keys_file = artms_data_ph_keys, 
                                  prot_exp =  "PH")

(To learn more about these testing datasets, check the documentation by running ?artms_data_ph_keys or ?artms_data_ph_evidence on the R console)

Once the QC is done, go to the folder "/path/to/your/working/directory/" and check out all the generated QC (pdf) files.

How to Contribute to artMS

artMS is an open source project, therefore you are more than welcome to contribute and make the analysis of Mass Spectrometry data easier and better using this fantastic language and environment for statistical computing and graphics (i.e. R).

There are multiple options:

Tips

Do you need to remember the basics of markdown? Check out this fantastic link.

artMS Help available online

The vignette can also be accessed at http://artms.org



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artMS documentation built on April 14, 2021, 6 p.m.