Constrained linear projection for estimating cell mixture or related coefficients.
projectMix(Y, Xmat, nonnegative=TRUE, sumLessThanOne=TRUE, lessThanOne=!sumLessThanOne)Matrix (m CpGs x n Subjects) of DNA methylation beta values
Matrix (m CpGs x K cell types) of cell-type specific methylomes
All coefficients >=0?
Coefficient rows should sum to less than one?
Every value should be less than one (but possibly sum to value greater than one)?
Projection coefficients resulting from constrained projection
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.
Houseman EA, Accomando WP et al. DNA methylation arrays as surrogate measures of cell mixture distribution, BMC Bioinformatics, 2012.