abagen.io.read_microarray¶
- abagen.io.read_microarray(fname, copy=False, parquet=True)[source]¶
Loads MicroarrayExpression.csv file found at fname
Microarray files contain raw expression data for all the tissue samples taken from a single donor across all genetic probes.
- Parameters
fname (str) – Path to MicroarrayExpression.csv file
copy (bool, optional) – Whether to return a copy if fname is a pre-loaded pandas.Dataframe. Default: False
parquet (bool, optional) – Whether to load data from parquet file instead of CSV. If a parquet file does not already exist then one will be created for faster loading in the future. Only available if
fastparquet
andpython-snappy
module are installed. Default: True
- Returns
microarray – Dataframe containing microarray expression data, where P is probes and S is samples. The row index is the unique probe ID assigned during processing, which can be used to match data to the information obtained with
read_probes()
. The column index is the unique sample ID (integer, beginning at 0) which can be used to match data to the information obtained withread_annotation()
.- Return type
(P, S) pandas.DataFrame