as {pbcmc} | R Documentation |
PAM50
high level coerce functionsThese 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.
as(object,Class,strict=TRUE,ext=possibleExtends(thisClass,Class)) as.PAM50(object) ## S4 method for signature 'MAList' as.PAM50(object)
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 |
Basically the $M and $genes items are copied into a MolecularPermutationClassifier's exprs and annotation slots respectively. In addition, if present, $targets content is also copied to the same named slot.
a PAM50 object with the respective copied data.
Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar
PAM50
for a complete example.
Other PAM50: classify,PAM50-method
,
filtrate,PAM50-method
,
pam50centroids
,
permutate,PAM50-method
,
subjectReport,PAM50-method
,
subtypes,PAM50-method
##Example 1: Create a PAM50 object ----------------------------------------- ##1) Just an empty object object<-PAM50() object ##2) Using Breast Cancer NKI database, if available. if(requireNamespace("breastCancerNKI")){ object<-loadBCDataset(Class=PAM50, libname="nki", verbose=TRUE) object ##Now we can inspect the object head(exprs(object)) ##The gene expression head(annotation(object)) ##The available annotation head(targets(object)) ##The clinical data present in the package } ##Example 2: Build a PAM50 object with user data -------------------------- ##Option 1: using PAM50 constructor. The user will only need: ##a) The M gene expression object, i. e., gene in rows and sample in columns ##b) The annotation data.frame which must include the compulsory fields ## "probe", "NCBI.gene.symbol" and "EntrezGene.ID" M<-pam50$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