reduce_dim: reduce_dim

In ddiez/scmisc: Miscellaneus Tools for the Analysis of Single Cell Data

reduce_dim

Description

reduce_dim

Usage

reduce_dim(x, method = "pca", dims = 2, ...)

## S3 method for class 'SingleCellExperiment'
reduce_dim(
  x,
  method = "pca",
  dims = 2,
  assay.name = "logcounts",
  coord.name = method,
  perplexity = NULL,
  initial_dims = 50,
  ...
)

## S3 method for class 'matrix'
reduce_dim(
  x,
  method = "pca",
  dims = 2,
  perplexity = 30,
  initial_dims = 50,
  ...
)

Arguments

x	matrix object.
method	tyoe of dimensionality reduction: pca, tsne, umap.
dims	number of dimensions to keep in final result.
...	arguments to be passed down to methods.
assay.name	name of assay slot.
coord.name	name of reducedDim slot.
perplexity	perplexity for tSNE.
initial_dims	initial PCA dimensions for tSNE.

ddiez/scmisc documentation built on July 21, 2024, 11:35 a.m.