DEprot.timecourse class

DEprot.timecourse class

Slots

results

data.frame with one row per protein: statistics, kinetic descriptors, cluster assignment and ranking. Class: "ANY".

fitted.curves

named list of matrices (proteins x grid points), one element per group level ('all' when no group was used). Class: "ANY".

time.grid

numeric vector of the prediction grid positions, expressed on the ORIGINAL time scale. Class: "ANY".

observed.means

named list of matrices (proteins x timepoints) with the mean measured value at each timepoint. Class: "ANY".

timepoints

numeric vector of the observed timepoints. Class: "ANY".

counts.used

matrix of the counts effectively analyzed (only the samples kept). Class: "ANY".

tc.metadata

metadata of the samples used in the time course (subset of the original DEprot@metadata). Class: "ANY".

sample.subset

vector containing the list of samples analyzed. Class: "ANY".

data.used

vector indicating the type of counts used (imputed, normalized, raw). Class: "ANY".

design

model matrix used by limma for the fit. Class: "ANY".

clusters

list with the membership matrix, the centroids, the method, the number of clusters and the fuzzifier. NULL when the clustering was not performed. Class: "ANY".

params

list of all the parameters used for the analysis. Class: "ANY".

profile.plot

ggplot object corresponding to the output of plot.timecourse.profiles for this object. Class: "ANY".