RefFreeEWAS (version 2.2)

RefFreeCellMixArray: Initialize Reference-Free Cell Mixture Projection

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

Value

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

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.

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

# NOT RUN {
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))
# }