DEprot.sPLSDA class

DEprot.sPLSDA class

Slots

sPLSDA.metadata

metadata of the samples used in the model (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".

group.column

string indicating the metadata column holding the classes that the model discriminates. Class: "ANY".

groups

factor of the classes, in the same order as the samples. Class: "ANY".

splsda

object of class mixo_splsda corresponding to the full output of mixOmics::splsda. It keeps the original mixOmics orientation of the components. Class: "ANY".

plsda

object of class mixo_plsda corresponding to the companion non-sparse model, fitted on the same data and used to rank all the proteins. Class: "ANY".

components

data.frame combining the sample scores and the metadata table, useful for replotting. Class: "ANY".

loadings

data.frame of the loadings of the sparse model, one row per protein and component, with the class in which each selected protein is the highest (contrib.group). Class: "ANY".

full.loadings

data.frame of the loadings and of the VIP scores of the non-sparse model, covering every protein of the matrix. This is the table used to build a ranking for a GSEA. Class: "ANY".

selected.proteins

named list of the proteins retained on each component. Class: "ANY".

importance

summary table of the proportion of variance explained by each component, for the protein block (X) and for the class block (Y). Class: "ANY".

counts.used

the counts matrix (log2) effectively used to fit the model, after the removal of the proteins carrying no information. Class: "ANY".

tuning

list with the grid of keepX tested, the cross-validated error over that grid and the values retained; NULL when keepX was provided by the user. Class: "ANY".

performance

list with the cross-validated error rates, the selection frequencies across the folds and the AUC; NULL when validate = FALSE. Class: "ANY".

cumulative.plot

ggplot object corresponding to the output of plot.sPLSDA.cumulative for this object. Class: "ANY".

scatter.plot.123

patchwork object combining the comp1-vs-comp2 and comp3-vs-comp2 scatters. Class: "ANY".

tuning.plot

ggplot object showing the error over the keepX grid; NULL when no tuning was performed. Class: "ANY".

performance.plot

ggplot object showing the cross-validated error per number of components; NULL when no validation was performed. Class: "ANY".

parameters

list of the parameters used to fit the model. Class: "ANY".