Authors: Lieven Clement and Olivier Thas
flowFDA is an R package for analysing flow cytometry experiments with model based clustering, functional principal component analysis, functional discriminant analysis and to compare multivariate flow cytometry fingerprints accross treatments (De Roy, K., Clement, L., Thas, O., Wang, Y., and Boon, N. (2012). Flow cytometry for fast microbial community fingerprinting. Water Research, 46 (3), 907-919.). It will be released on R/Bioconductor in the future. The package is developed at Ghent University.
Install flowFDA from its GitHub repository. You first need to install the R/Bioconductor packages Biobase, BiocGenerics (>= 0.1.6), [flowCore] (http://bioconductor.org/packages/release/bioc/html/flowCore.html), flowViz, flowFP, graphics, grDevices, methods, stats, stats4, MASS, multcomp,mclust and devtools.
source("https://bioconductor.org/biocLite.R")
biocLite(c("flowCore", "flowViz", "flowFP", "MASS", "multcomp","mclust","devtools")Then install flowFDAE using the install_github function in the
devtools package. (With
build_vignettes=TRUE, the vignettes will be built and installed.)
You first need to install the flowFDADataExample package for this purpose
library(devtools)
install_github("lievenclement/flowFDAExampleData")
install_github("lievenclement/flowFDA", build_vignettes=TRUE)###Vignettes Examples can be found in the vignettes
Regular analysis: vignette("flowFDA")
Analysis based on probability binning for backward compatibility with De Roy et al. (2012), Water Research, 46(3), 907-919: vignette("flowFDAProbabilityBinning")
Copyright (C) 2016 Lieven Clement and Olivier Thas.
The flowFDA package as a whole is distributed under GPL-3 (GNU General Public License version 3).