Cell Mixture Projection (reference-based)
Constrained linear projection for estimating cell mixture or related coefficients.
projectMix(Y, Xmat, nonnegative=TRUE, sumLessThanOne=TRUE, lessThanOne=!sumLessThanOne)
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)? |
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.
Projection coefficients resulting from constrained projection
E. Andres Houseman
Houseman EA, Accomando WP et al. DNA methylation arrays as surrogate measures of cell mixture distribution, BMC Bioinformatics, 2012.
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