FetchH5: Fetch data from the hdf5 file

In zh542370159/SCP: Single Cell Pipeline

Fetch data from the hdf5 file

Description

This function fetches data from an hdf5 file. It can fetch gene expression data, metadata, and reduction data from the specified file and returns a Seurat object.

Usage

FetchH5(
  DataFile,
  MetaFile,
  name = NULL,
  features = NULL,
  slot = NULL,
  assay = NULL,
  metanames = NULL,
  reduction = NULL
)

Arguments

DataFile	The path to the hdf5 file containing the data.
MetaFile	The path to the hdf5 file containing the metadata.
name	The name of the dataset in the hdf5 file. If not specified, the function will attempt to find the shared group name in both files.
features	The names of the genes or features to fetch. If specified, only these features will be fetched.
slot	The slot for the counts in the hdf5 file. If not specified, the first slot will be used.
assay	The name of the assay to use. If not specified, the default assay in the hdf5 file will be used.
metanames	The names of the metadata columns to fetch.
reduction	The name of the reduction to fetch.

Value

A Seurat object with the fetched data.

See Also

CreateDataFile CreateMetaFile PrepareSCExplorer RunSCExplorer

Examples

## Not run: 
data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
srt <- FetchH5(
  DataFile = "./SCExplorer/Data.hdf5",
  MetaFile = "./SCExplorer/Meta.hdf5",
  features = c("Ins1", "Ghrl"),
  metanames = c("SubCellType", "Phase"),
  reduction = "UMAP"
)
CellDimPlot(srt, group.by = c("SubCellType", "Phase"), reduction = "UMAP")
FeatureDimPlot(srt, features = c("Ins1", "Ghrl"), reduction = "UMAP")

## End(Not run)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.