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