scITD (version 1.0.4)

subset_scMinimal: 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
)

Value

A subsetted scMinimal object.

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)

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)