The SafeQuant Package includes methods for analysis of quantitative (LFQ,TMT,HRM) Proteomics data.
A) Install CRAN library dependencies (open R)
R> install.packages(c("seqinr","gplots","corrplot","optparse","data.table","epiR","ggplot2","magrittr","dplyr","ggrepel"))
B) Install BioConductor library dependencies (open R)
R> source("http://bioconductor.org/biocLite.R")
R> biocLite(c("limma","Biobase","pcaMethods","impute","GO.db","UniProt.ws","affy"))
Option 1, install "master branch" using "devtools"
Make sure you have a working development environment.
Windows: Install Rtools.
Mac: Install Xcode from the Mac App Store.
Linux: Install a compiler and various development libraries (details vary across different flavors of Linux).
R> install.packages("devtools")
R> library(devtools)
R> install_github("eahrne/SafeQuant")
Option 2, install latest CRAN version
R> install.packages("SafeQuant")
A) locate file safeQuant.R (C:\Users\ahrnee-adm\Downloads\SafeQuant\exec\safeQuant.R ) This is the SafeQuant main script. Copy it to an appropriate directory, e.g. c:\Program Files\SafeQuant\
B) open terminal To display help options
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -h
To run (with minimal arguments)
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -i "c:\Program Files\SafeQuant\testData\peptide_measurement.csv" -o "c:\Program Files\SafeQuant\out"
Input file: "Peptide Measurement" .CSV file
Input file: "Raw Export" .XLS
Note that the experimental design needs to be specified (column numbers refer to listing order in .txt).
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -i ../../SafeQuantTestData/TMT_10-Plex_Scaffold_Raw_Export_Example.xls --EX 1,2,3,4,5:6,7,8,9,10
Input file: proteinGroups.txt
Note that the experimental design needs to be specified (column numbers refer to listing order in .txt).
> Rscript "c:\Program Files\SafeQuant\safeQuant.R" -i ../../SafeQuantTestData/misc/maxQuant/proteinGroups.txt --EX 1,2,3:6,7,8
Smyth, G. K. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol, 3 SP -, Article3. http://www.ncbi.nlm.nih.gov/pubmed/16646809
https://raw.githubusercontent.com/eahrne/SafeQuant/master/inst/manuals/SafeQuant_UseCases.txt
https://github.com/eahrne/SafeQuant/blob/master/inst/manuals/tsv_spreadsheet_help.pdf
https://github.com/eahrne/SafeQuant/blob/master/inst/manuals/SafeQuant-man.pdf
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