reduce_dims_scExp {ChromSCape}R Documentation

Reduce dimensions (PCA, TSNE, UMAP)

Description

Reduce dimensions (PCA, TSNE, UMAP)

Usage

reduce_dims_scExp(
  scExp,
  dimension_reductions = c("PCA", "TSNE", "UMAP"),
  n = 50,
  batch_correction = FALSE,
  batch_list = NULL,
  verbose = TRUE
)

Arguments

scExp

A SingleCellExperiment object.

dimension_reductions

A character vector of methods to apply. (c('PCA','TSNE','UMAP'))

n

Numbers of dimensions to keep for PCA. (50)

batch_correction

Do batch correction ? (FALSE)

batch_list

List of characters. Names are batch names, characters are sample names.

verbose

(TRUE)

Value

A SingleCellExperiment object containing feature spaces. See ?reduceDims().

Examples


scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)
scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP"))
scExp = normalize_scExp(scExp)
scExp = reduce_dims_scExp(scExp,dimension_reductions=c("PCA","UMAP"))
[Package ChromSCape version 1.0.0 Index]