pbcmc (version 1.0.0)

filtrate,PAM50-method: filtrate centroid genes from PAM50 classification

Description

Remove exprs rows not required by MolecularPermutationClassifier subclasses to classify samples, in this case PAM50. This means to only keep genes with valid EntrezGeneID, i. e., not NA and present in PAM50 signature centroids. In addition, annotation slot will only keep "probe", "EntrezGene.ID" and "NCBI.gene.symbol" fields required by genefu's intrinsic.cluster.predict function.

Usage

"filtrate"(object, verbose = getOption("verbose", default =    FALSE))

Arguments

object

a PAM50 object.

verbose

should the user feedback be displayed? By default value is "verbose" global option parameter, if present, or FALSE otherwise.

Value

MolecularPermutationClassifier subclass with updated slots:

@exprs

only rows required by the classifier.

@annotation

consistent with exprs rows and only "probe", "EntrezGene.ID" and "NCBI.gene.symbol" annotation fields.

See Also

PAM50 for a complete example.

Other PAM50: as, classify,PAM50-method, pam50centroids, permutate,PAM50-method, subjectReport,PAM50-method, subtypes,PAM50-method

Examples

##Using pam50centroids package example data
data(pam50centroids)
pam50centroids
pam50centroids<-filtrate(pam50centroids, verbose=TRUE)   
pam50centroids

##Using Breast Cancer NKI database, if available.  
if(requireNamespace("breastCancerNKI")){
    object<-loadBCDataset(Class=PAM50, libname="nki", verbose=TRUE)  
    object
    object<-filtrate(object, verbose=TRUE)   
    object
}