The goal of MetabolomicsBasics is to provide a set of functions toinvestigate raw data (a matrix of intensity values) from (metabol)omicsexperiments, i.e. following peak picking and signal deconvolution.Functions can be used toi.e.:
A detailed description of best practice usage may be found in thepublicationhttps://link.springer.com/protocol/10.1007/978-1-4939-7819-9_20.
You can install the development version of MetabolomicsBasics fromGitHub with:
# install.packages("devtools")devtools::install_github("janlisec/MetabolomicsBasics")A typical use case would be to compute a Principal ComponentAnalysis:
raw<- MetabolomicsBasics::rawsam<- MetabolomicsBasics::samMetabolomicsBasics::RestrictedPCA(dat = raw,sam = sam,group.col ="Group",legend.x ="bottomleft",medsd =TRUE,fmod ="Group")
Moreelaborate plots, like the polar coordinate visualization of heterosispattern are possible:
x<-t(raw)colnames(x)<- sam$GTMetabolomicsBasics::PolarCoordHeterPlot(x=x,gt=c("B73","B73xMo17","Mo17"),plot_lab="graph",col=1:10,thr=0.5,rev_log=exp(1))#> Parameter 'col' should be a color vector of length nrow(x)