Array of reference-free cell-mixture decompositions of a DNA methylation data set, with custom initialization
RefFreeCellMixArrayWithCustomStart(Y,mu.start,Klist=1:5,iters=10,
Yfinal=NULL,verbose=FALSE)Matrix (m CpGs x n Subjects) of DNA methylation beta values
matrix of starting values for Mu: number of columns must be at least the maximum in Klist
List of K values (each K = assumed number of cell types)
Number of iterations to execute for each value of K
Matrix (m* CpGs x n Subjects) of DNA methylation beta values on which to base final methylomes
Report summary of errors after each iteration for each fit?
List, each element is an object of S3 class RefFreeCellMix, containing the last iteration of Mu and Omega.
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.
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.