RefFreeCellMixInitialize

Matrix (m CpGs x n Subjects) of DNA methylation beta values

Distance matrix (object of class "dist") to use for clustering.

Y.Distance

Hiearchical clustering object (from hclust function)

Y.Cluster

OK to calculate distance matrix for large number of subjects? (See details.)

largeOK

Method for calculating distance matrix

dist.method

Additional parameters for hclust function

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Initializes the methylome matrix "Mu" for RefFreeCellMix

Reference-free method for conducting EWAS while deconvoluting DNA methylation
arising as mixtures of cell types. The older method
(Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to
surrogate variable analysis (SVA and ISVA), except that it makes additional use
of a biological mixture assumption.
The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar
to non-negative matrix factorization, with additional constraints
and additional utilities.

RefFreeCellMixInitialize: Initialize Reference-Free Cell Mixture Projection

Description

Usage

Arguments

Value

Details

See Also