genefu (version 2.4.2)

claudinLow: Claudin-low classification for Breast Cancer Data

Description

Subtyping method for identifying Claudin-Low Breast Cancer Samples. Code generously provided by Aleix Prat.

Usage

claudinLow(x,classes="",y,nGenes="",priors="equal",std=F,distm="euclidean",centroids=F)

Arguments

x

the data matrix of training samples, or pre-calculated centroids

classes

a list labels for use in coloring the points

y

the data matrix of test samples

nGenes

the number of genes selected when training the model

priors

'equal' assumes equal class priors, 'class' calculates them based on proportion in the data

std

when true, the training and testing samples are standardized to mean=0 and var=1

distm

the distance metric for determining the nearest centroid, can be one of euclidean, pearson, or spearman

centroids

when true, it is assumed that x consists of pre-calculated centroids

References

Aleix Prat, Joel S Parker, Olga Karginova, Cheng Fan, Chad Livasy, Jason I Herschkowitz, Xiaping He, and Charles M. Perou (2010) "Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer", Breast Cancer Research, 12(5):R68

See Also

medianCtr, claudinLowData

Examples

data(claudinLowData)

#Training Set
train<-claudinLowData
train$xd<- medianCtr(train$xd)
# Testing Set
test<-claudinLowData
test$xd<- medianCtr(test$xd)

# Generate Predictions
predout<-claudinLow(train$xd, as.matrix(train$classes$Group,ncol=1), test$xd)

# Obtain results
results <- cbind(predout$predictions, predout$distances)
#write.table(results,"T.E.9CELL.LINE_results.txt",sep="\t",col=T, row=F)