write_h5files: Write R object to .h5 Files

In duohongrui/simutils: Common functions used in data simulation and evaluation

Write R object to .h5 Files

Description

This function facilitates the progress of converting any R object into .h5 file to store information and read it in Python easily.

Usage

write_h5files(data, file_path = NULL)

.write_h5files(h5file, data, name = NULL)

Arguments

data	The data remain to be write
file_path	The file path of the h5file. Default is NULL and h5 file will be generated automatically
h5file	A new h5 file
name	Default is NULL. One of the names of a list.

Value

An h5 file

Examples

# Generate a matrix
set.seed(1)
ref_data <- matrix(rpois(n = 10^4, lambda = 0.5), nrow = 1000)
colnames(ref_data) <- paste0("cell_", 1:ncol(ref_data))
rownames(ref_data) <- paste0("gene_", 1:nrow(ref_data))

# Generate a sparse matrix
sparse_matrix <- Matrix::Matrix(data = ref_data, sparse = TRUE)

# Generate a dataframe
df <- as.data.frame(sparse_matrix)

# Generate a list
x <- list("length" = 2,
          "integer" = 2L,
          "logical" = TRUE,
          "sparse_matrix" = sparse_matrix,
          "df" = df,
          "matrix" = ref_data)

# Set a path
file_path <- tempfile(fileext = ".h5")
# Write an h5 file
write_h5files(x, file_path = file_path)
# Load the h5 file
file.h5 <- hdf5r::H5File$new(file_path, mode = "r")

duohongrui/simutils documentation built on March 12, 2024, 8:40 p.m.