aggregateFeatures {scDblFinder}R Documentation

aggregateFeatures

Description

Aggregates similar features (rows).

Usage

aggregateFeatures(
  x,
  dims.use = seq(2L, 12L),
  k = 1000,
  num_init = 2,
  use.mbk = NULL,
  use.subset = 5000,
  use.TFIDF = TRUE,
  ...
)

Arguments

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 mbkmeans). If NULL, the minibatch approach will be used if there are more than 30000 features.

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 mbkmeans. Can for instance be used to pass the 'BPPARAM' argument for multithreading.

Value

An aggregated version of 'x' (either an array or a 'SingleCellExperiment', depending on the input).


[Package scDblFinder version 1.8.0 Index]