RefFreeEWAS (version 2.2)

RefFreeCellMixInitializeBySVD: Initialize Reference-Free Cell Mixture Projection by SVD

Description

Initialize Reference-Free Cell Mixture Projection by SVD

Usage

RefFreeCellMixInitializeBySVD(Y, type=1)

Arguments

Y

Matrix (m CpGs x n Subjects) of DNA methylation beta values

type

See details

Value

Matrix of starting values for Mu.

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.

See Also

RefFreeCellMix, RefFreeCellMixArrayWithCustomStart

Examples

# NOT RUN {
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))
# }