ReadH5: Load data from an HDF5 File

In mojaveazure/seurat-disk: Interfaces for HDF5-Based Single Cell File Formats

Load data from an HDF5 File

Description

HDF5 allows storing data in an arbitrary fashion, which makes reading data into memory a hassle. The methods here serve as convenience functions for reading data stored in a certain format back into a certain R object. For details regarding how data should be stored on disk, please see the h5Seurat file specification.

Usage

## S3 method for class 'H5D'
as.array(x, ...)

## S3 method for class 'H5D'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S3 method for class 'H5Group'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S4 method for signature 'H5Group'
as.factor(x)

## S4 method for signature 'H5Group'
as.list(x, which = NULL, ...)

## S3 method for class 'H5D'
as.logical(x, ...)

## S3 method for class 'H5D'
as.matrix(x, transpose = FALSE, ...)

## S3 method for class 'H5Group'
as.matrix(x, ...)

## S3 method for class 'H5D'
as.sparse(x, verbose = TRUE, ...)

## S3 method for class 'H5Group'
as.sparse(x, ...)

## S3 method for class 'H5D'
dimnames(x)

Arguments

x	An HDF5 dataset or group
...	Arguments passed to other methods
row.names	NULL or a character vector giving the row names for the data frame. Missing values are not allowed.
optional	logical. If TRUE, setting row names and converting column names (to syntactic names: see make.names) is optional. Note that all of R's base package as.data.frame() methods use optional only for column names treatment, basically with the meaning of data.frame(*, check.names = !optional). See also the make.names argument of the matrix method.
transpose	Transpose the data upon reading it in, used when writing data in row-major order (eg. from C or Python)

Value

as.array: returns an array with the data from the HDF5 dataset

as.data.frame: returns a data.frame with the data from the HDF5 dataset or group

as.factor: returns a factor with the data from the HDF5 group

as.list: returns a list with the data from the HDF5 group

as.logical: returns a logical with the data from the HDF5 dataset

as.matrix, H5D method: returns a matrix with the data from the HDF5 dataset

as.sparse, H5D method: returns a sparse matrix with the data from the HDF5 dataset

as.sparse, as.matrix, H5Group method: returns a sparseMatrix with the data from the HDF5 group

dimnames: returns a two-length list of character vectors for row and column names. Row names should be in a column named index

mojaveazure/seurat-disk documentation built on Nov. 5, 2023, 9:40 a.m.