myRefFreeCellMix: Replicate the function RefFreeCellMix() from RefFreeEWAS...

In ziyili20/TOAST: Tools for the analysis of heterogeneous tissues

Replicate the function RefFreeCellMix() from RefFreeEWAS package

Description

Replicate the function RefFreeCellMix() from RefFreeEWAS package (https://cran.r-project.org/web/packages/RefFreeEWAS/index.html) as that package is not in CRAN anymore

Usage

myRefFreeCellMix(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?

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.

Value

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.

ziyili20/TOAST documentation built on Aug. 28, 2022, 11:28 a.m.