TCGA module survial_init error
Opened this issue · 1 comments
Describe the bug
When I followed the tutorial of TCGA module with TCGA-BRCA data, an error emerged in the step of aml_tcga.survial_init().
To Reproduce
Steps to reproduce the behavior:
- Follow the tutorial
- Run aml_tcga.survial_init()
- See error
Screenshots
`---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[12], line 1
----> 1 aml_tcga.survial_init()
File ~/.conda/envs/omicverse/lib/python3.11/site-packages/omicverse/bulk/_tcga.py:99, in pyTCGA.survial_init(self)
97 pd_c=self.clinical_sheet
98 for i in pd_c.index:
---> 99 if pd_c.loc[i,'vital_status'].iloc[0]=='Alive':
100 day_li.append(pd_c.loc[i,'days_to_last_follow_up'].iloc[0])
101 elif pd_c.loc[i,'vital_status'].iloc[0]=='Dead':
AttributeError: 'str' object has no attribute 'iloc'`
Hi,
This erroe look like pd_c.loc[i,'vital_status']
is not a pd.Series
. It seems that need a strict judgements when value is ''
.
Sincerely