MolecularPermutationClassifierGetseters: Accessors for MolecularPermutationClassifier child class...

In pbcmc: Permutation-Based Confidence for Molecular Classification

Description

Slot setters/getters for MolecularPermutationClassifier hierarchy classes

Usage

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)

Arguments

object	MolecularPermutationClassifier subclass object
value	according to the function call: parameters: named list with at least the following fields: $nPerm integer with number of permutations. Default: 1e4L $where character with significant value used. Default value is "fdr". $pCutoff numeric with p-value or fdr cutoff used, i.e., variable<pCutoff. Default: 0.01 $corCutoff numeric with correlation difference between classes cutoff used, i.e., |ρ(profile,class_A)-ρ(profile,class_B)|>corCutoff $keep should null distribution simulation values be kept?. Default: FALSE annotation: data.frame with individual annotations (genes, etc). Minimal compulsory fields are: $probe same characters as in row.names(M). $EntrezGene.ID integer with NCBI Entrez Data Base. $NCBI.gene.symbol character with gene mnemonic, a.k.a. gene symbol. exprs: matrix with gene exprs profile, where genes are in rows and subjects as columns, a.k.a., M matrix. targets: data.frame with additional subject data.
...	additional parameters according to function call.

Value

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:

$class

factor with with all possible class levels.

permutation

named list with at least the following fields:

pvalues

numeric matrix with subjects in row and classes in columns.

$fdr

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.

Author(s)

Cristobal Fresno [e-mail], German A. Gonzalez [e-mail], Andrea S. Llera [e-mail] and Elmer Andres Fernandez [e-mail]

See Also

PAM50 for a complete example.

Other MolecularPermutationClassifier: MolecularPermutationClassifier-class, show

Examples

##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  

pbcmc documentation built on Nov. 1, 2018, 2:09 a.m.