Reading and writing

Reading and writing#

General I/O#

io.read_csv

Read a comma-separated values (csv) file into an EHRData object.

io.read_h5ad

Read a hdf5 (h5ad) file into an EHRData object.

io.read_zarr

Read a zarr store into an EHRData object.

io.write_h5ad

Write EHRData objects to an hdf5 file.

io.write_zarr

Write EHRData objects to disk.

io.from_pandas

Transform a given DataFrame into an EHRData object.

io.to_pandas

Transform an EHRData object to a DataFrame.

OMOP CDM#

io.omop.setup_connection

Setup a connection to the OMOP CDM database.

io.omop.setup_obs

Setup the observation table for EHRData object.

io.omop.setup_variables

Extracts selected tables of a data-point character from the OMOP CDM.

io.omop.setup_interval_variables

Extracts selected tables of a time-span character from the OMOP CDM.