access_data_seurat: Extract cell-level meta data and count matrix from Seurat...

In byzhang23/TreeCorTreat: Tree-based correlation screen for phenotype-associated transcriptomic features and cell types

Extract cell-level meta data and count matrix from Seurat object

Description

Extract cell-level meta data and count matrix from Seurat object

Usage

access_data_seurat(seurat_obj, reduction = "umap", output_dir)

Arguments

seurat_obj	A Seurat object
reduction	Extract x,y coordinates from a type of dimension reduction. If run default harmony_integration() function, can be one of 'umap' (default) or 'harmony'.
output_dir	An output directory

Value

A list of filtered inputs:

• count: a filtered count matrix

• cell_meta: a cell-level metadata

• phylo_tree: phylogenetic tree

Author(s)

Boyang Zhang <[e-mail]>, Hongkai Ji

Examples

## Not run: 
access_data_seurat(seurat_object,reduction = 'umap')

## End(Not run)

byzhang23/TreeCorTreat documentation built on May 7, 2024, 8:37 a.m.