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R
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inst/extdata
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DESCRIPTION
LICENSE
NAMESPACE
NEWS
README
matchWeiz.Rproj

README

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.