totalVI_load: Load totalVI output from adata object into...

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

Load totalVI output from adata object into SingleCellExperiment

Description

Load totalVI output from adata object into SingleCellExperiment

Usage

totalVI_load(
  adata,
  sce = NULL,
  reducedDim_include = c("totalVI", "X_umap"),
  RNA_layer = "denoised_rna",
  barcodes = intersect,
  protein_obsm = "denoised_protein",
  protein_fg_obsm = "protein_fg_prob",
  protein_altexp_name = "VI_ADT",
  protein_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
RNA_layer	Name of adata$layers that contains the scVI normalized expression matrix
barcodes	Function to handle if different barcodes are included in either SCE or adata objects? Intersect to include only barcodes present in both objects, union to include all barcodes - will fill missing values with NA and missing expression with 0 (default: intersect)
protein_obsm	Name of adata$obsm that contains the totalVI protein denoised expression matrix
protein_fg_obsm	Name of adata$obsm that contains the totalVI protein foreground probability matrix
protein_altexp_name	Name of altExp to place totalVI protein data
protein_rownames_prefix	Prefix for rownames in altExp containing totalVI protein data
...	Passed on to scVI_load
reducedDims	Which reducedDims should be transferred from adata$obsm

Value

Returns a SingleCellExperiment (SCE). If existing sce is not given the returned SCE contains totalVI normalized expression, else totalVI normalized expression and totalVI protein expression are added as altExps

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