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", "UMAP"),
  n = 50,
  batch_correction = FALSE,
  batch_list = NULL,
  remove_PC1 = FALSE,
  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.

remove_PC1

Remove PC1 before UMAP & T-SNE, as probably correlated to library size ? Recommended when using 'TFIDF' normalization method. (FALSE)

verbose

Print messages ?(TRUE)

Value

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

Examples


raw <- create_scDataset_raw()
scExp = create_scExp(raw$mat, raw$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 1.4.0 Index]