pbcmc (version 1.0.0)

classify,PAM50-method: 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

"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.

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)