RefFreeCellMixArrayWithCustomStart: Reference-Free Cell Mixture Projection - Custom...
In RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution

Description Usage Arguments Details Value Author(s) References See Also

Array of reference-free cell-mixture decompositions of a DNA methylation data set, with custom initialization

1 2	RefFreeCellMixArrayWithCustomStart(Y,mu.start,Klist=1:5,iters=10, Yfinal=NULL,verbose=FALSE)

`Y`	Matrix (m CpGs x n Subjects) of DNA methylation beta values
`mu.start`	matrix of starting values for Mu: number of columns must be at least the maximum in Klist
`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?

List of Reference-free decompositions for a range of K values. For each value of K, the decomposition is initialized by using the first K columns of mu.start. 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.

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

E. Andres Houseman

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.

RefFreeCellMix, RefFreeCellMixInitializeBySVD

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