Seurat_SpatialRNA: Convert Seurat object to SpatialRNA object

In Feng-Zhang/RNAseqFlow:

Convert Seurat object to SpatialRNA object

Description

Convert Seurat class to SpatialRNA class as the input data for RCTD analysis using spacexr package.

Usage

Seurat_SpatialRNA(
  seurat,
  slot = "counts",
  assay = "Spatial",
  image = NULL,
  nUMI_name = "nCount_Spatial"
)

Arguments

seurat	A Seurat class object.
slot	Specific assay data to get or set. see SeuratObject::GetAssayData() for detail information.
assay	Specific assay to get data from or set data for; defaults to the default assay. see SeuratObject::GetTissueCoordinates() for detail information.
image	Name of SpatialImage object to get coordinates for; if NULL, will attempt to select an image automatically. see SeuratObject::GetTissueCoordinates() for detail information.
nUMI_name	Optional, a colname (by pixel barcode) in Seurat object, which refer to total counts or UMI's appearing at each pixel. If not provided, nUMI will be assumed to be the total counts appearing on each pixel.

Feng-Zhang/RNAseqFlow documentation built on Sept. 10, 2022, 7:13 a.m.