aggregateFeatures {scDblFinder} | R Documentation |
Aggregates similar features (rows).
aggregateFeatures( x, dims.use = seq(2L, 12L), k = 1000, num_init = 2, use.mbk = NULL, use.subset = 5000, use.TFIDF = TRUE, ... )
x |
A integer/numeric (sparse) matrix, or a 'SingleCellExperiment' including a 'counts' assay. |
dims.use |
The PCA dimensions to use for clustering rows. |
k |
The approximate number of meta-features desired |
num_init |
The number of initializations used for k-means clustering. |
use.mbk |
Logical; whether to use minibatch k-means (see
|
use.subset |
How many cells (columns) to use to cluster the features. |
use.TFIDF |
Logical; whether to use TFIDF normalization (instead of standard normalization) to assess the similarity between features. similarity |
... |
Passed to |
An aggregated version of 'x' (either an array or a 'SingleCellExperiment', depending on the input).