myprojectMix: Replicate the function myprojectMix() from RefFreeEWAS...

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

Replicate the function myprojectMix() from RefFreeEWAS package

Description

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

Usage

myprojectMix(Y, Xmat, nonnegative=TRUE, sumLessThanOne=TRUE, lessThanOne=!sumLessThanOne)

Arguments

Y	Matrix (m CpGs x n Subjects) of DNA methylation beta values
Xmat	Matrix (m CpGs x K cell types) of cell-type specific methylomes
nonnegative	All coefficients >=0?
sumLessThanOne	Coefficient rows should sum to less than one?
lessThanOne	Every value should be less than one (but possibly sum to value greater than one)?

Details

Function for projecting methylation values (Y) onto space of methyomes (Xmat), with various constraints. This is the reference-based method described in Houseman et al. (2012) and also appearing in the minfi package.

Value

Projection coefficients resulting from constrained projection

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