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

    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 1.2.62 Index]