def read_data(self):
# Real Data #
# process RNA-seq expression data
gene_exp, gene_name_map = rp.process(args.patient_data)
# convert entrez gene id to uniprot id
pat_ids = gene_exp.columns.values # patient TCGA ids
ent_ids = gene_exp.index.values # gene entrez ids
log('num_pat:', pat_ids.shape)
return gene_exp.values, pat_ids, ent_ids
def read_rnaseq_data(self):
# Real Data #
# process RNA-seq expression data
gene_exp, gene_name_map = rp.process(self.args.rnaseq_patient_data, self.args.continuous, self.args.threshold)
# convert entrez gene id to uniprot id
pat_ids = gene_exp.columns.values # patient TCGA ids
ent_ids = gene_exp.index.values # gene entrez ids
return gene_exp.values, pat_ids, ent_ids
def read_data(self):
# Real Data #
# process RNA-seq expression data
gene_exp, gene_name_map = rp.process(args.rnaseq_data)
# convert entrez gene id to uniprot id
pat_ids = gene_exp.columns.values # patient TCGA ids
for i in range(len(pat_ids)):
pat_ids[i] = '-'.join(pat_ids[i].split('-')[0:3])
return pat_ids