G'day,
I've added a new peak detector to the Chromatogram deconvolution module
(in Peak list methods > Peak detection). Set the Algorithm parameter to
Wavelets (XCMS).
The Wavelets detector relies on Bioconductor's XCMS package for R.
Therefore, you must have R v2.15 or later installed. To install the XCMS
package, run R and issue the following commands:
source("http://bioconductor.org/biocLite.R";)
biocLite("xcms")
To run R from MZmine the rJava package [3] must be installed in R, so
also run the following R command:
install.package("rJava")
You will also need to correctly configure several environment variables
in your MZmine start-up script (startMZmine_Windows.bat,
startMZmine_Linux.sh or startMZmine_MacOSX.command):
R_HOME
This is the directory where R is installed, e.g. for Windows it will be
something like C:\Program Files\R\R-2.15.0.
R_LIBS_USER
This is the directory in which R installs third-party packages. It's
usually a sub-directory of your personal directory, e.g. for Windows it
will be something like %USERPROFILE%\Documents\R\win-library\2.15.
PATH
Append the directory that contains R's libraries. It will be a
sub-directory of %R_HOME%, e.g. for 32-bit Windows it will be something
like %R_HOME%\bin\i386 or for 64-bit Windows %R_HOME%\bin\x64.
JRI_LIB_PATH
This is the directory where rJava has installed its JRI libraries. It
will be a sub-directory of %R_LIBS_USER%, e.g. for 32-bit Windows it
will be something like %R_LIBS_USER%\rJava\jri\i386 or for64-bit Windows
%R_LIBS_USER%\rJava\jri\x64.
Regards,
Chris.
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