def generate_TCGA_LUAD_MessengerRNA():
data = MessengerRNA(
data=os.path.join(cohort_folder_path, "LUAD__geneExp.txt"),
transpose=True,
usecols="GeneSymbol|TCGA",
gene_index="GeneSymbol",
gene_level="gene_name",
)
data.drop_genes(data.expressions.columns[50:])
data.drop_samples(data.expressions.index[:100])
return data
def generate_TCGA_LUAD_MessengerRNA_dask():
data = MessengerRNA(
data=os.path.join(cohort_folder_path, "LUAD__geneExp.txt"),
transpose=True,
usecols="GeneSymbol|TCGA",
gene_index="GeneSymbol",
gene_level="gene_name",
npartitions=4,
)
data.drop_genes(data.expressions.columns[50:])
data.initialize_annotations(index="gene_name", gene_list=None)
return data