RefFreeCellMixArray: Initialize Reference-Free Cell Mixture Projection

In RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution

Description

Array of reference-free cell-mixture decompositions of a DNA methylation data set

Usage

RefFreeCellMixArray(Y,Klist=1:5,iters=10,Yfinal=NULL,verbose=FALSE, 
   dist.method = "euclidean",...)

Arguments

Y	Matrix (m CpGs x n Subjects) of DNA methylation beta values
Klist	List of K values (each K = assumed number of cell types)
iters	Number of iterations to execute for each value of K
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 for each fit?
dist.method	Method for calculating distance matrix for methylome initialization
...	Additional parameters for hclust function for methylome initialization

Details

List of Reference-free decompositions for a range of K values. For each value of K, the decomposition is initialized by hierarchical clutering as specified by the parameters dist.method, etc. Note that for each K, 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.

Value

List, each element is an object of S3 class RefFreeCellMix, containing the last iteration of Mu and Omega.

Author(s)

E. Andres Houseman

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

RefFreeCellMix

Examples

data(HNSCC)
Y.shortTest <- Y.HNSCC.averageBetas[1:500,]
testArray2  <- RefFreeCellMixArray(Y.shortTest,Klist=1:5,iters=5)
sapply(testArray2,deviance,Y=Y.shortTest)

## Not run: 
testBootDevs <- RefFreeCellMixArrayDevianceBoots(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)

RefFreeEWAS documentation built on May 2, 2019, 5:52 a.m.