Usage Arguments

PlotGroups Function for plotting gene expression profile at different experimental groups Description This function displays the gene expression profile for each experimental group in a time series gene expression experiment. Arguments data vector or matrix containing the gene expression data edesign matrix describing experimental design. Rows must be arrays and columns experiment descriptors time vector indicating time assigment for each array groups matrix indicating experimental group to which each array is assigned repvect index vector indicating experimental replicates show.fit logical indicating whether regression fit curves must be plotted dis regression design matrix step.method stepwise regression method to fit models for cluster mean profiles. It can be either "backward", "forward", "two.ways.backward" or "two.ways.forward" min.obs minimal number of observations for a gene to be included in the analysis alfa significance level used for variable selection in the stepwise regression nvar.correction argument for correcting stepwise regression significance level. See T.fit summary.mode the method to condensate expression information when more than one gene is present in the data. Possible values are "representative" and "median" 1 2 PlotGroups show.lines logical indicating whether a line must be drawn joining plotted data points for reach group groups.vector vector indicating experimental group to which each variable belongs xlab label for the x axis cex.xaxis graphical parameter maginfication to be used for x axis in plotting functions ylim range of the y axis main plot main title cexlab graphical parameter maginfication to be used for x axis label in plotting functions legend logical indicating whether legend must be added when plotting profiles sub plot subtitle Details To compute experimental groups either a edesign object must be provided, or separate values must be given for the time, repvect and groups arguments. When data is a matrix, the average expression value is displayed. When there are array replicates in the data (as indicated by repvect), values are averaged by repvect. PlotGroups plots one single expression profile for each experimental group even if there are more that one genes in the data set. The way data is condensated for this is given by summary.mode. When this argument takes the value "representative", the gene with the lowest distance to all genes in the cluster will be plotted. When the argument is "median", then median expression value is computed. When show.fit is TRUE the stepwise regression fit for the data will be computed and the regression curves will be displayed. If data is a …