\name{TDARACNE} \Rdversion{1.1} \alias{TDARACNE} %- Also NEED an '\alias' for EACH other topic documented here. \title{ TDARACNE } \description{ Main function, see P. Zoppoli, S. Morganella, M. Ceccarelli. TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 2010, 11:154. } \usage{ TDARACNE(eSet,N,delta=3,likehood=1.2,norm=2,logarithm=1,thresh=0,ksd=1,tolerance=0.15,plot=FALSE,dot=FALSE,name="youHaveForgottenIt",adj=FALSE) } %- maybe also 'usage' for other objects documented here. \arguments{ \item{eSet}{ %% ~~Describe \code{eSet} here~~ eSet is the ExpressionSet object } \item{N}{ %% ~~Describe \code{N} here~~ N is respectively the number of bins in percentile normalization or in rank normalization } \item{delta}{ %% ~~Describe \code{delta} here~~ delta is the maximum time delay allowed to infer connections } \item{likehood}{ %% ~~Describe \code{likehood} here~~ likehood is the fold change used as threshold to state the initial change expression (IcE) } \item{norm}{ %% ~~Describe \code{norm} here~~ if you want column percentile normalization put norm == 1; if you want Rank normalization put norm == 2; } \item{logarithm}{ %% ~~Describe \code{logarithm} here~~ if z is log put logarithm == 0; } \item{thresh}{ %% ~~Describe \code{thresh} here~~ the Influence threshold. if you have a threshold and a SD put them here in this format: c(thresh,SD) if you don't have threshold put 0 in thresh; } \item{ksd}{ %% ~~Describe \code{ksd} here~~ ksd is the standard deviation multiplier; } \item{tolerance}{ %% ~~Describe \code{tolerance} here~~ tolerance is the DPI tolerance; 0 means no tolerance 1 means no DPI 0.15 is the default ARACNE tolerance as it is for TDARACNE } \item{plot}{ %% ~~Describe \code{plot} here~~ plot must be TRUE to obtain automatically the graph } \item{dot}{ %% ~~Describe \code{dot} here~~ dot must be TRUE to obtain a .dot file } \item{name}{ %% ~~Describe \code{name} here~~ name must be written with quotation marks(like this:'examplename') and is the name of the .dot file produced; } \item{adj}{ %% ~~Describe \code{adj} here~~ adj must be TRUE to obtain an adjacent matrix } } \examples{ ## take paper data library(TDARACNE) data(dataIRMAon) data(threshIRMAon) ## main function; in output gives to you and adj matrix and a .dot file # eSet is the ExpressionSet object # N is respectively the number of bins in percentile normalization or in rank normalization # delta is the maximum time delay allowed to infer connections # likehood is the fold change used as threshold to state the initial change expression (IcE) # if you want column percentile normalization put norm == 1; # if you want Rank normalization put norm == 2; # if z is log put logarithm == 0; # if you don't have threshold put 0 in thresh; # ksd is the standard deviation multiplier; # tolerance is the DPI tolerance; # plot must be TRUE to obtain automatically the graph # dot must be TRUE to obtain a .dot file # name must be written with quotation marks(like this:'examplename') and is the name of the .dot file produced; # adj must be TRUE to obtain an adjacent matrix TDARACNE(dataIRMAon,11,"netIRMAon",delta=3,likehood=1.2,norm=2,logarithm=1,thresh=threshIRMAon,ksd=0,tolerance=0.15); } % Add one or more standard keywords, see file 'KEYWORDS' in the % R documentation directory.