Computes the transformation matrix Chat used to map from observed
data to latent space, based on a pseudo-inverse of the prior annotation
matrix. Optionally standardizes the columns
of priorMat before computing.
getChat(priorMat, scale = TRUE)
Arguments
- priorMat
A numeric or sparse matrix (features x pathways)
containing prior annotations.
- scale
Logical; if TRUE (default), standardizes the columns
of priorMat
before computing Chat.
Value
A numeric matrix Chat of dimensions (pathways x features).
Examples
# simple toy prior: 3 features x 2 pathways
priorMat <- matrix(
c(
1, 0, 1,
0, 1, 0
),
nrow = 3, ncol = 2,
dimnames = list(
paste0("gene", seq_len(3)),
paste0("path", seq_len(2))
)
)
# compute Chat (2 pathways x 3 features)
Chat <- getChat(priorMat)
#> Inverting...
#> done