RefFreeEWAS (version 2.2)

RefFreeCellMix: Reference-Free Cell Mixture Projection

Description

Reference-free cell-mixture decomposition of DNA methylation data set

Usage

RefFreeCellMix(Y,mu0=NULL,K=NULL,iters=10,Yfinal=NULL,verbose=TRUE)

Arguments

Y

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

mu0

Matrix (m CpGs x K cell types) of *initial* cell-type specific methylomes

K

Number of cell types (ignored if mu0 is provided)

iters

Number of iterations to execute

Yfinal

Matrix (m* CpGs x n Subjects) of DNA methylation beta values on which to base final methylomes

verbose

Report summary of errors after each iteration?

Value

Object of S3 class RefFreeCellMix, containing the last iteration of Mu and Omega.

Details

Reference-free decomposition of DNA methylation matrix into cell-type distributions and cell-type methylomes, Y = Mu Omega^T. Either an initial estimate of Mu must be provided, or else the number of cell types K, in which case RefFreeCellMixInitialize will be used to initialize. Note that the decomposition will be based on Y, but Yfinal (=Y by default) will be used to determine the final value of Mu based on the last iterated value of Omega.

References

Houseman, E. Andres, Kile, Molly L., Christiani, David C., et al. Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. BMC bioinformatics, 2016, vol. 17, no 1, p. 259.

See Also

RefFreeCellMixInitialize

Examples

# NOT RUN {
data(HNSCC)

# Typical use
Y.shortTest <- Y.HNSCC.averageBetas[1:500,]
Y.shortTest.final <- Y.HNSCC.averageBetas[1:1000,]
testArray1  <- RefFreeCellMixArray(Y.shortTest,Klist=1:3,iters=5,Yfinal=Y.shortTest.final)
testArray1
lapply(testArray1,summary)
sapply(testArray1,deviance,Y=Y.shortTest.final)

# Example with explicit initialization
testKeq2  <- RefFreeCellMix(Y.shortTest, mu0=RefFreeCellMixInitialize(Y.shortTest,K=2))
testKeq2
head(testKeq2$Mu)
head(testKeq2$Omega)
# }