Correlations in NMF Models
basiscor computes the correlation matrix between
basis vectors, i.e. the columns of its basis
matrix – which is the model's first matrix factor.
profcor computes the correlation matrix between
basis profiles, i.e. the rows of the coefficient
matrix – which is the model's second matrix factor.
basiscor(x, y, ...) profcor(x, y, ...)
Each generic has methods defined for computing
correlations between NMF models and/or compatible
matrices. The computation is performed by the base
function cor.
signature(x = "NMF", y =
"matrix"): Computes the correlations between the basis
vectors of x and the columns of y.
signature(x = "matrix", y =
"NMF"): Computes the correlations between the columns of
x and the the basis vectors of y.
signature(x = "NMF", y = "NMF"):
Computes the correlations between the basis vectors of
x and y.
signature(x = "NMF", y =
"missing"): Computes the correlations between the basis
vectors of x.
signature(x = "NMF", y = "matrix"):
Computes the correlations between the basis profiles of
x and the rows of y.
signature(x = "matrix", y = "NMF"):
Computes the correlations between the rows of x
and the basis profiles of y.
signature(x = "NMF", y = "NMF"):
Computes the correlations between the basis profiles of
x and y.
signature(x = "NMF", y =
"missing"): Computes the correlations between the basis
profiles of x.
# generate two random NMF models a <- rnmf(3, 100, 20) b <- rnmf(3, 100, 20) # Compute auto-correlations basiscor(a) profcor(a) # Compute correlations with b basiscor(a, b) profcor(a, b) # try to recover the underlying NMF model 'a' from noisy data res <- nmf(fitted(a) + rmatrix(a), 3) # Compute correlations with the true model basiscor(a, res) profcor(a, res) # Compute correlations with a random compatible matrix W <- rmatrix(basis(a)) basiscor(a, W) identical(basiscor(a, W), basiscor(W, a)) H <- rmatrix(coef(a)) profcor(a, H) identical(profcor(a, H), profcor(H, a))
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