This software provides the source code of the R package flowPeaks The printer friendly version of this file is part of the vignette pdf file located at flowPeaks/inst/doc/flowPeaks-guide.pdf in the source package or located at flowPeaks/doc/flowPeaks-guide of the installed flowPeaks library or Windows built library. 1. Licensing Under the Artistic License, you are free to use and redistribute this software. However, we ask you to cite the following paper if you use this software for publication Ge and Sealfon, flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding, Bioinformatics, 2012, In Press 2 Overview We combine the ideas from the finite mixture model and histogram spatial exploration together to find the clustering of the flow cytometry data. This new algorithm, in which we called flowPeaks, can be applied to high dimensional data and identify irregular shape clusters. The algorithm first uses K-means algorithm with a large K to partition the population into many compact clusters. These partitioned data allow us to generate a smoothed density function. All local peaks are exhaustively found by exploring the density function and the cells are clustered by the associated local peak. The algorithm fowPeaks is automatic, fast and reliable and robust to the cluster shape and outliers. Details can be seen in the paper by Ge (2012). 3 Installation 3.1 All users When you are reading this and find the R package is already available in the Bioconductor package repository. You can install it directly from the Bioconductor. --Windows users: select the menu "Packages" and then click "Select repositories..." and choose "BioC software". And then select the menu "Packages", click "install R package(s)..." and then look for the package flowPeaks --Linux users: This also works for Windows users. Type the following after you have invoked R > source("http://bioconductor.org/biocLite.R") > biocLite("flowPeaks") If this succeeds, congratulations. 3.2 Windows Users Please read section 3.1 to install the R package from Bioconductor before proceeding this. If you have the prebuilt binary of flowPeaks zip file, you can install the package by selecting the menu "Packages", and then "Install packages from a local zip file", and then point to prebuilt binary of flowPeaks zip file. To build flowPeaks from the source by using Rtools is very not straightforward. R novices are not encouraged to try this. Experienced R users need to carefully follow the instruction of the Rtools (http://www.murdoch-sutherland.com/Rtools/) and http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset. The GSL library needs to be downloaded from the file local215.zip at http://www.stats.ox.ac.uk/pub/Rtools/goodies/multilib/. The top folder (top_path_local) of the extracted file local215.zip should contain three subfolders: include, share and lib. The next step is to modify the file flowPeaks/src/Makevar.win as below. PKG_LIBS += -L(top_path_local)/lib/$(R_ARCH)/ -lgsl -lgslcblas -lm PKG_CXXFLAGS += -I(top_path_local)/include The users are not encouraged to compile their own gsl library by MinGW or Visual Studio. Most likely their own version of gsl library is not going to work. 3.3 Linux Users To build the flowPeaks package from the source, make sure that the following is present on your system. C++ compiler GNU Scientific Library (GSL) A C++ compiler is needed to build the package as the core function is coded in C++. GSL can be downloaded directly from http://www.gnu.org/software/gsl/ and follow its instructions to install the GSL from the source code. Alternatively, GSL can also be installed from your linux specific package manager (for example, Synaptic Package Manager for Ubuntu system). Other than the GSL binary library, please make sure the GSL development package is also installed, which includes the header files when building flowPeaks package. Now you are ready to install the package: R CMD INSTALL flowPeaks_x.y.z.tar.gz If GSL is installed at some non-standard location such that it cannot be found when installing flowPeaks. You need to do the following 1. Find out the GSL include location (<path-to-include>) where the GSL header files are stored in the sub folder gsl, and GSL library location (<path-to-lib>) where the lib files are stored. If the GSL's gsl_config can be run, you can get them easily by gsl-config --cflags and gsl-config --libs 2. In the file flowPeaks/src/Makevars, you may need to change the last two lines as below PKG_CXXFLAGS = -I<path-to-include> PKG_LIBS = -L<path-to-lib>