myRefFreeCellMixInitialize: Replicate the function RefFreeCellMixInitialize() from...

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

Replicate the function RefFreeCellMixInitialize() from RefFreeEWAS package

Description

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

Usage

myRefFreeCellMixInitialize(Y,K=2,Y.Distance=NULL, Y.Cluster=NULL,
    largeOK=FALSE, dist.method = "euclidean", ...)

Arguments

Y	Matrix (m CpGs x n Subjects) of DNA methylation beta values
K	Number of cell types
Y.Distance	Distance matrix (object of class "dist") to use for clustering.
Y.Cluster	Hiearchical clustering object (from hclust function)
largeOK	OK to calculate distance matrix for large number of subjects? (See details.)
dist.method	Method for calculating distance matrix
...	Additional parameters for hclust function

Details

Initializes the methylome matrix "Mu" for RefFreeCellMix by computing the mean methylation (from Y) over K clusters of Y, determined by the Y.Cluster object. If Y.Cluster object does not exist, it will be created from Y.Distance (using additional clustering parameters if supplied). If Y.Distance does not exist, it will be created from t(Y). As a protection against attempting to fit a very large distance matrix, the program will stop if the number of columns of Y is > 2500, unless largeOK is explicitly set to TRUE.

Value

An m x K matrix of mean methylation values.

Author(s)

E. Andres Houseman

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