Initialize Reference-Free Cell Mixture Projection
Array of reference-free cell-mixture decompositions of a DNA methylation data set
RefFreeCellMixArray(Y,Klist=1:5,iters=10,Yfinal=NULL,verbose=FALSE, dist.method = "euclidean",...)
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 |
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.
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.
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)
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