ProteinAtlas

class openomics.database.annotation.ProteinAtlas(path='https://www.proteinatlas.org/download/', file_resources=None, col_rename={'Ensembl': 'gene_id', 'Gene': 'protein_name'}, blocksize=0, verbose=False)

Bases: openomics.database.base.Database

Loads the database from .

Default path: . Default file_resources: {

“”: “”, “”: “”, “”: “”,

}

Attributes Summary

COLUMNS_RENAME_DICT

Methods Summary

get_expressions([index, type])	Returns (NX) expressions from the proteinatlas.tsv table.
load_dataframe(file_resources[, blocksize])	param file_resources

Attributes Documentation

COLUMNS_RENAME_DICT = {'Ensembl': 'gene_id', 'Gene': 'protein_name'}

Methods Documentation

get_expressions(index='gene_name', type='Tissue RNA')

Returns (NX) expressions from the proteinatlas.tsv table. :param index: a column name to index by. If column contain multiple values, then aggregate by median values. :param type: one of {“Tissue RNA”, “Cell RNA”, “Blood RNA”, “Brain RNA”, “RNA - “}. If “RNA - “, then select all types of expressions.

Parameters

• index –

• type –

Returns

Return type

expressions (pd.DataFrame)

load_dataframe(file_resources, blocksize=None)

Parameters

• file_resources –

• blocksize –