reduce_dims_scExp: Reduce dimensions (PCA, TSNE, UMAP)

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

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"))

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.