scVI_load: Load scVI output from adata object into SingleCellExperiment

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

Load scVI output from adata object into SingleCellExperiment

Description

Load scVI output from adata object into SingleCellExperiment

Usage

scVI_load(
  adata,
  sce = NULL,
  obs_ignore = c("_scvi_labels", "_scvi_batch"),
  obs_include = "all",
  obs_overwrite = FALSE,
  obs_prefix = "",
  barcodes = intersect,
  reducedDim_prefix = "",
  reducedDim_include = c("X_scVI", "X_umap"),
  reducedDimNames_replace = "^X_",
  RNA_layer = "scvi_normalized",
  altexp_name = "VI_RNA",
  rownames_prefix = "VI_"
)

Arguments

adata	AnnData object containing scVI output
sce	Existing sce object. If supplied, coldata is added to this object and scVI normalized expression is added as an altExp
obs_ignore	Which columns in adata$obs should be ignored before importing?
obs_include	Which columns in adata$obs should be included (default "all")
obs_overwrite	Should columns existing in the sce be overwritten?
obs_prefix	Prefix obs columns before importing
barcodes	Function to handle if different barcodes are included in either SCE or adata objects? Intersect to include only barcodes present in both objects, union to include all barcodes - will fill missing values with NA and missing expression with 0 (default: intersect)
reducedDim_prefix	Prefix reducedDim names before adding to sce
reducedDim_include	Which reducedDims should be transferred from adata$obsm
reducedDimNames_replace	String to replace in obsm names before adding to the sce (removes "^X_" by default)
RNA_layer	Name of adata$layers that contains the scVI normalized expression matrix
altexp_name	Name of altExp to place scVI normalized SCE object if existing sce is supplied
rownames_prefix	Prefix for rownames in scVI normalized SCE

Value

Returns a SingleCellExperiment (SCE). If existing sce is not given the returned SCE contains scVI normalized expression, else scVI normalized expression is added as an altExp

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.