This class helps dealing with h5ad objects from Python AnnData. You have
several options will allow for retrieval of the underlying data.
Methods
Method new()
Initialises the Anndata Parser.
Arguments
h5_pathString. Path to the h5 file.
Returns
Returns the initialised class.
Method get_obs_table()
Returns the observation table with all the data from the
h5ad file.
Usage
AnnDataParser$get_obs_table()
Returns
data.table. The found observations are returned. The pandas index
will be named sample_id. Remaining columns (if found) will be returned
as factors due to the way the data is stored in h5.
Method get_var_info()
Returns the variable table with all the data from the
h5ad file.
Usage
AnnDataParser$get_var_info()
Returns
data.table. The found observations are returned. The pandas index
will be named var_id. Remaining columns (if found) will be returned as
factors due to the way the data is stored in h5.
Method get_raw_counts()
Returns the counts that are stored in X slot of the
anndata object.
Usage
AnnDataParser$get_raw_counts()
Returns
Returns the count matrix with samples = columns and rows =
features.
Method get_key_data()
Wrapper function that returns a list of the stored count
data and the metadata found in the h5ad file.
Usage
AnnDataParser$get_key_data()
Returns
List with following elements:
metadata - metadata from the respective h5ad file
var_info - metadata on the variables from the respective h5ad
file.
counts - counts that were found in the h5ad file.
Method clone()
The objects of this class are cloneable with this method.
Usage
AnnDataParser$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.