Fetch data from the hdf5 file and returns a Seurat object
Usage
FetchH5(
data_file,
meta_file,
name = NULL,
features = NULL,
layer = NULL,
assay = NULL,
metanames = NULL,
reduction = NULL,
verbose = TRUE
)Arguments
- data_file
The path to the hdf5 file containing the data.
- meta_file
The path to the hdf5 file containing the metadata.
- name
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.
- layer
The layer for the counts in the hdf5 file. If not specified, the first layer will be used.
- assay
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
Reduction to fetch.
- verbose
Whether to print the message. Default is
TRUE.
Examples
if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
srt <- FetchH5(
data_file = "./SCExplorer/data.hdf5",
meta_file = "./SCExplorer/meta.hdf5",
features = c("Ins1", "Ghrl"),
metanames = c("SubCellType", "Phase"),
reduction = "UMAP"
)
} # }