filtrate,PAM50-method {pbcmc} | R Documentation

## `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

    ## S4 method for signature 'PAM50'
    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.

### Author(s)

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

### 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
    }

[Package pbcmc version 1.8.0 Index]