write_h5: The scRNAs-seq analysis objec to H5

In JiekaiLab/RIOH5: The scRNA-seq data IO between R and Python(R version)

Description

Write h5 and the scRNA-seq analysis object converted to h5

Usage

write_h5(
  data,
  file,
  object.type = "seurat",
  assay.name = "RNA",
  save.graphs = FALSE
)

Arguments

data	The scRNA-seq analysis object data.
file	The h5 file
object.type	Denotes which object to save.Available options are: "seurat": converted the "seurat object" to the h5 file. "singlecellexperiment": converted the "singlecellexperiment object" to the h5 file. "monocle": converted the "monocle3 object" to 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.