Description Usage Arguments Value References
This function is used to automatically select the optimal
contrastive parameter and L1 penalty term for scPCA based on a clustering
algorithm and average silhouette width. Analogous to fitGrid
,
but replaces all lapply
calls by
bplapply
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
target |
The target (experimental) data set, in a standard format such
as a |
target_valid |
A holdout set of the target (experimental) data set, in a
standard format such as a |
center |
A |
scale |
A |
c_contrasts |
A |
contrasts |
A |
penalties |
A |
n_eigen |
A |
alg |
A |
clust_method |
A |
n_centers |
A |
max_iter |
A |
linkage_method |
A |
clusters |
A |
eigdecomp_tol |
A |
eigdecomp_iter |
A |
A list similar to that output by prcomp
:
rotation - the matrix of variable loadings
x - the rotated data, centred and scaled, if requested, data multiplied by the rotation matrix
contrast - the optimal contrastive parameter
penalty - the optimal L1 penalty term
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