reduce_dimension: Performs dimension reduction and adds results to the given...

In jenzopr/singlecellutils: Utility functions for single-cell data

Description

See details for available dimension reduction techniques that can be applied to the object.

Usage

reduce_dimension(object, flavor = c("umap", "som", "asvd", "isomds",
  "rsvd"), slot = flavor, ...)

Arguments

object	A SingleCellExperiment object.
flavor	Determines which dimension reduction technique to apply.
slot	Determines which entry of the reducedDims slot to use for reduced embedding.
...	Additional parameters passed to functions.

Details

The following dimension reduction techniques are available:

• UMAP - Uniform Manifold Approximation and Projection, see umap.

• approximate SVD - see approximate_svd

• randomized SVD - see randomized_svd

• Multidimensional scaling - see isomds

• Self-organizing maps - see scSOM

Value

A SingleCellExperiment object with modified reducedDims slot.

Examples

## Not run: 
# Apply UMAP on normalized expression values, but store results in a slot called dimred_umap.
obj <- reduce_dimension(obj, flavor = "umap", slot = "dimred_umap", exprs_values = "norm_exprs")

# Apply randomized SVD on normalized expression values, keeping 50 dimensions, followed by umap.
# Using magrittr pipes, the result of randomized SVD is stored in the rsvd slot and
# picked up by umap.
obj %<>%
  reduce_dimension(flavor = "rsvd", exprs_values = "norm_exprs", n_dims = 50) %>%
  reduce_dimension(flavor = "umap", exprs_values = NULL, use_dimred = "rsvd")

## End(Not run)

jenzopr/singlecellutils documentation built on June 12, 2019, 2:51 a.m.