Initialize Reference-Free Cell Mixture Projection by SVD
Initialize Reference-Free Cell Mixture Projection by SVD
RefFreeCellMixInitializeBySVD(Y, type=1)
Y |
Matrix (m CpGs x n Subjects) of DNA methylation beta values |
type |
See details |
This method initializes the reference-free cell mixture deconvolution using an ad-hoc method based on singular value decomposition. Type=1 will attempt to discretize Mu to 0/1, Type=2 will attempt to find a continuous range using column ranks. However, neither of these strategies is guaranteed to result in stable starting values for K larger than the "true" value of K.
Matrix of starting values for Mu.
E. Andres Houseman
data(HNSCC)
Y.shortTest <- Y.HNSCC.averageBetas[1:500,]
mu.start.svd <- RefFreeCellMixInitializeBySVD(Y.shortTest)
testArray2 <- RefFreeCellMixArrayWithCustomStart(Y.shortTest, mu.start=mu.start.svd,
Klist=1:3,iters=5)
sapply(testArray2,deviance,Y=Y.shortTest)
## Not run:
testBootDevs <- RefFreeCellMixArrayBySVDDevianceBoots(testArray2,Y.shortTest,R=10)
testBootDevs
apply(testBootDevs[-1,],2,mean,trim=0.25)
which.min(apply(testBootDevs[-1,],2,mean,trim=0.25))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.