claudinLow {genefu} | R Documentation |
Subtyping method for identifying Claudin-Low Breast Cancer Samples. Code generously provided by Aleix Prat.
claudinLow(x, classes="", y, nGenes="", priors="equal", std=FALSE, distm="euclidean", centroids=FALSE)
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 |
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
data(claudinLowData) #Training Set train <- claudinLowData train$xd <- medianCtr(train$xd) # Testing Set test <- claudinLowData test$xd <- medianCtr(test$xd) # Generate Predictions predout <- claudinLow(x=train$xd, classes=as.matrix(train$classes$Group,ncol=1), y=test$xd) # Obtain results results <- cbind(predout$predictions, predout$distances) #write.table(results,"T.E.9CELL.LINE_results.txt",sep="\t",col=T, row=F)