classify,PAM50-method {pbcmc} | R Documentation

## `classify` subjects with PAM50 molecular signature

### Description

Obtain PAM50 subtype using genefu centroid Spearman's correlation implementation. If std=="median" probes with the same mapping are averaged. Then, the complete database is center normalized using gene median expression. This is done in order to assure selecting the same "gene" to those in "genefu" library, instead of the most variant probe (default in geneid.map), when more than one probe match the same gene. This selection is based on probe population variance that could depends on the number of accounted genes.

### Usage

    ## S4 method for signature 'PAM50'
    classify(object, std = c("none", "scale", "robust",
        "median")[1], verbose = getOption("verbose", default = FALSE))

### Arguments

`object` | a MolecularPermutationClassifier subclass object.
`std` | character to select standardization alternative "none" (default), "scale" and "robust" as in genefu original implementation, plus the suggested "median" if many subjects are available.
`verbose` | should the user feedback be displayed? By default value is "verbose" global option parameter, if present, or FALSE otherwise.

### Value

a PAM50 object with the updated slots:

`@exprs` | updated matrix with the used std parameter.
`@classification` | $subtype subject named factor with all classifier possible levels, i.e, "Basal", "Her2", "LumA", "LumB" and "Normal". $probability numeric matrix with subtype class probability for each subject, as in genefu, obtained as the positive proportion of correlation explained by each subtype. $correlation numeric matrix with Spearman's rho correlation of each subject to the corresponding PAM50 subtypes.

### 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

### References

1. Haibe-Kains B, Schroeder M, Bontempi G, Sotiriou C and Quackenbush J, 2014, genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. R package version 1.16.0, www.pmgenomics.ca/bhklab/

2. Perou CM, Sorlie T, Eisen MB, et al., 2000, Molecular portraits of human breast tumors. Nature 406:747-752.

3. Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PB., 2010, Clinical implementation of the intrinsic subtypes of breast cancer, The Lancet Oncology 11(8):718-719.

### See Also

`PAM50` for a complete example.

Other PAM50: `as`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subjectReport,PAM50-method`, `subtypes,PAM50-method`

### Examples

    ##Using pam50centroids package example data
    data(pam50centroids)

    ##Get the original PAM50 calls using genefu implementation
    pam50centroids<-classify(pam50centroids, std="none", verbose=TRUE)
    classification(pam50centroids)

[Package pbcmc version 1.8.0 Index]