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Add fetcher for Gryglewski et al., 2018 expression maps
The issue
There was a really nice paper last year by Gryglewski et al., 2018 that used some variogram modelling to generate "smooth" microarray expression maps for all the genes with valid Entrez IDs from the AHBA dataset. They've generously made these maps available online for download.
Proposed solution
I'm proposing a new function in abagen.datasets
that lets people fetch maps for a given gene, provided they have the Entrez ID:
def fetch_gryglewski_map(entrez, data_dir=None, resume=True, verbose=1):
"""
Fetches expression maps from [DS2]_ for gene with Entrez ID `entrez`
Parameters
----------
entrez : int
Entrez ID of gene for which to fetch expression map
data_dir : str, optional
Directory where data should be downloaded and unpacked. Default:
current directory
resume : bool, optional
Whether to resume download of a partly-downloaded file. Default: True
verbose : int, optional
Verbosity level (0 means no message). Default: 1
Returns
-------
maps : dict
Dictionary with keys ['vol', 'vol_mirror', 'surf', 'surf_mirror'],
where corresponding values are lists of filepaths to downloaded Nifti
(volumetric) and MGH (surface) files.
References
----------
.. [DS2] Gryglewski, G., Seiger, R., James, G. M., Godbersen, G. M.,
Komorowski, A., Unterholzner, J., ... & Kasper, S. (2018). Spatial analysis
and high resolution mapping of the human whole-brain transcriptome for
integrative analysis in neuroimaging. NeuroImage, 176, 259-267.
"""
# fetch and return dictionary with files for specified map
# can use other abagen.datasets.fetch_X functions as models