subset_scMinimal: Subset an scMinimal object by specified genes, donors, cells,...

In scITD: Single-Cell Interpretable Tensor Decomposition

Subset an scMinimal object by specified genes, donors, cells, or cell types

Description

Subset an scMinimal object by specified genes, donors, cells, or cell types

Usage

subset_scMinimal(
  scMinimal,
  ctypes_use = NULL,
  cells_use = NULL,
  donors_use = NULL,
  genes_use = NULL,
  in_place = TRUE
)

Arguments

scMinimal	environment A sub-container for the project typically consisting of gene expression data in its raw and processed forms as well as metadata
ctypes_use	character The cell types to keep (default=NULL)
cells_use	character Cell barcodes for the cells to keep (default=NULL)
donors_use	character The donors to keep (default=NULL)
genes_use	character The genes to keep (default=NULL)
in_place	logical If set to TRUE then replaces the input object with the new subsetted object (default=TRUE)

Value

A subsetted scMinimal object.

Examples

cell_names <- colnames(test_container$scMinimal_full$count_data)
cells_sub <- sample(cell_names,40)
scMinimal <- subset_scMinimal(test_container$scMinimal_full,
cells_use=cells_sub)

scITD documentation built on Sept. 8, 2023, 5:11 p.m.