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R package MatchWeiz This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. How to install package dependencies: ## Note: try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("Rdisop") install.packages("fdrtool") ## install the latest (>=1.0.8) version of the CHNOZS package: install.packages("CHNOSZ") ## In case this doesn't work on MacOS. A possible solution is to compile ## and install from source, with first manually install gfortran and add the aliases to the R env.: ## curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 ## sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C / ## mkdir -p ~/.R ## touch ~/.R/Makevars ## Next, add these aliases into 'Makevars': ## F77="gfortran-4.8" ## FC="gfortran-4.8" ## Compile and install CHNOSZ from source: ## install.packages("CHNOSZ", repos="http://R-Forge.R-project.org",type="source") ## The 'devtools' package is required to install directly from GitHub install.packages("devtools") library("devtools") install_github("AharoniLab/MatchWeiz") ## Usage examples are available inside the R package help files for individual functions. ## start help by: "help(package="matchWeiz")" ## Preparation the "stdMix" (i.e., the mix of chemical standards used by the software for retention time correction) The individual stock solutions of the chemical standards were prepared at a concentration of 1 mg/ml in methanol, with the following exceptions: 1) Stocks of L-Tryptophan and L-Tyrosine were prepared in 80%MeOH containing 2% formic acid as follows: first, formic acid was used for dilution, and then the corresponding amounts of water and methanol were added. 2) Stock of alpha-Tometin was prepared at a concentration of 0.5 mg/ml in MeOH. Next, all individual stock solutions were sonicated for 20 min in bath sonicator to improve dilution and equal volumes from each stock were combined together to form the stock-Mix solution. Finally, a working Std-Mix solution was prepared by diluting a stock-Mix solution 10-fold with methanol. The final concentrations of standards in the std-Mix solution are: 3.3 ug/ml for alpha-Tomatin and 6.6 ug/ml for all other compounds. ## The list of required chemical standards is specified in: "inst/extdata/StdMix.tsv", ## We recommend including a minimum of 10-12 of the specified chemical standards in the mix ## and injecting the mix at least 2-3 times over the experiment for effective RT correction.