as {pbcmc} | R Documentation

## `PAM50` high level coerce functions

### Description

These functions (setAs and as.PAM50) are intended to be used with limma `MAList-class` in order to coerce its structure into a compatible PAM50 class.

### Usage

    as(object,Class,strict=TRUE,ext=possibleExtends(thisClass,Class))

    as.PAM50(object)

    ## S4 method for signature 'MAList'
    as.PAM50(object)

### Arguments

`object` | MAList object with at least M and genes items, optionally targets.
`Class` | character with the name of class "PAM50" to be coerced.
`strict, ext` | see `as` function.

### Details

Basically the $M and $genes items are copied into a MolecularPermutationClassifier's exprs and annotation slots respectively. In addition, if present, $targets content is also copied to the same named slot.

### Value

a PAM50 object with the respective copied data.

### 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: `classify,PAM50-method`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subjectReport,PAM50-method`, `subtypes,PAM50-method`

### Examples

    ##Example 1: Create a PAM50 object -----------------------------------------
    ##1) Just an empty object
    object<-PAM50()
    object

    ##2) Using Breast Cancer NKI database, if available.
    if(requireNamespace("breastCancerNKI")){
        object<-loadBCDataset(Class=PAM50, libname="nki", verbose=TRUE)
        object
        ##Now we can inspect the object
        head(exprs(object))      ##The gene expression
        head(annotation(object)) ##The available annotation
        head(targets(object))    ##The clinical data present in the package
    }

    ##Example 2: Build a PAM50 object with user data --------------------------
    ##Option 1: using PAM50 constructor. The user will only need:
    ##a) The M gene expression object, i. e., gene in rows and sample in columns
    ##b) The annotation data.frame which must include the compulsory fields
    ## "probe", "NCBI.gene.symbol" and "EntrezGene.ID"
    M<-pam50$centroids
    genes<-pam50$centroids.map
    names(genes)<-c("probe", "NCBI.gene.symbol", "EntrezGene.ID")
    object<-PAM50(exprs=M, annotation=genes)
    object

    ##Option 2: Two ways to build it from a MAList (as or as.PAM50)-------------
    ##Let's use PAM50 classifier's centroids toy example, i. e., the five subject
    ##subtypes, which must correctly classify all the subject.
    M<-pam50$centroids
    genes<-pam50$centroids.map
    names(genes)<-c("probe", "NCBI.gene.symbol", "EntrezGene.ID")
    maux<-new("MAList", list(M=M, genes=genes))
    ##calling as function
    object<-as(maux, "PAM50")
    object
    ##same result with as.PAM50 function
    object<-as.PAM50(maux)
    object

[Package pbcmc version 1.8.0 Index]