seurat_write_h5: The seurat object to h5

Description Usage Arguments

View source: R/seuratIO.R

Description

The Seurat object is converted to the h5 file.

Usage

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seurat_write_h5(
  seurat = NULL,
  file = NULL,
  assay.name = NULL,
  save.graphs = FALSE
)

Arguments

seurat

The seurat object.

file

The h5 file.

assay.name

'assay.name' is used to flag the data type. Defualt is "RNA". Available options are:

  • "RNA": this is the scRNA-seq data.

  • "spatial": this is the spatial data.

save.graphs

Default is False , determing whether to save the graph(cell-cell similarity network). seurat graph is different from scanpy graph. Their relationship are set "distances": "knn", "connectivities": "snn" roughly.


JiekaiLab/RIOH5 documentation built on June 5, 2021, 8:37 a.m.