parameters {pbcmc} | R Documentation |
Slot setters/getters for MolecularPermutationClassifier hierarchy classes
parameters(object) ## S4 method for signature 'MolecularPermutationClassifier' parameters(object) parameters(object) <- value ## S4 replacement method for signature 'MolecularPermutationClassifier' parameters(object) <- value ## S4 method for signature 'MolecularPermutationClassifier' exprs(object) ## S4 replacement method for signature 'MolecularPermutationClassifier,ANY' exprs(object) <- value ## S4 method for signature 'MolecularPermutationClassifier' annotation(object, ...) ## S4 replacement method for signature 'MolecularPermutationClassifier,ANY' annotation(object) <- value targets(object) ## S4 method for signature 'MolecularPermutationClassifier' targets(object) targets(object) <- value ## S4 replacement method for signature 'MolecularPermutationClassifier' targets(object) <- value classification(object) ## S4 method for signature 'MolecularPermutationClassifier' classification(object) permutation(object) ## S4 method for signature 'MolecularPermutationClassifier' permutation(object)
object |
MolecularPermutationClassifier subclass object |
value |
according to the function call:
|
... |
additional parameters according to function call. |
according to function call one of the following objects:
parameters |
named list see value parameter |
exprs |
matrix with gene exprs profile, where genes are in rows and subjects as columns, a.k.a., M matrix. |
annotation |
data.frame see value parameter |
classification |
named list with at least the following fields: |
factor with with all possible class levels.
permutation |
named list with at least the following fields: |
numeric matrix with subjects in row and classes in columns.
numeric matrix with False Discovery Rate correction of pvalues by row.
parameters<- |
MolecularPermutationClassifier object with parameters updated slot. |
exprs<- |
MolecularPermutationClassifier object with exprs updated slot. |
annotation<- |
MolecularPermutationClassifier object with annotation updated slot. |
targets<- |
MolecularPermutationClassifier object with targets updated slot. |
Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar
PAM50
for a complete example.
Other MolecularPermutationClassifier:
MolecularPermutationClassifier-class
,
show
##Using pam50centroids package example data data(pam50centroids) ##Now we can inspect pam50centroids object head(exprs(pam50centroids)) ##The gene expression head(annotation(pam50centroids)) ##The available annotation head(targets(pam50centroids)) ##The clinical data present in the package ##Work with the parameters parameters(pam50centroids) ##Display them aux<-parameters(pam50centroids) aux$keep<-TRUE ##Set keep to FALSE parameters(pam50centroids)<-aux parameters(pam50centroids) ##Also exprs<-, annotation<- and targets<- available functions to update ##the respective slots