whitelist.subset.ls.Seurat: whitelist.subset.ls.Seurat

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

whitelist.subset.ls.Seurat

Description

Subsets cells in a list of Seurat objects based on an externally provided list of cell IDs.

Usage

whitelist.subset.ls.Seurat(
  ls.obj = ls.Seurat,
  metadir = p$cellWhiteList,
  whitelist.file = "NonStressedCellIDs.2020.10.21_18h.tsv"
)

Arguments

ls.obj	A list of Seurat objects. Default: ls.Seurat.
metadir	Directory for the metadata. Default: p$cellWhiteList.
whitelist.file	Filename of the whitelist containing cell IDs. Default: "NonStressedCellIDs.2020.10.21_18h.tsv".

Details

The function first validates the presence of all identities from the metadata in the Seurat objects. If all identities are present, the function subsets each Seurat object based on the whitelist of cell IDs.

Value

A list of Seurat objects containing only the cells specified in the whitelist.

See Also

subset

Examples

## Not run: 
if (interactive()) {
  ls.Seurat.subset <- whitelist.subset.ls.Seurat(
    ls.obj = ls.Seurat, metadir = p$"cellWhiteList",
    whitelist.file = "NonStressedCellIDs.2020.10.21_18h.tsv"
  )
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.