shappiron commited on
Commit
b48dead
·
verified ·
1 Parent(s): a33c36f

dataset exploration usage scenario added

Browse files
Files changed (1) hide show
  1. README.md +22 -0
README.md CHANGED
@@ -127,6 +127,8 @@ it can be either rounded by the researchers to full years, or converted from mon
127
 
128
  ## Usage Guidelines
129
 
 
 
130
  First install our nice [library](https://github.com/ComputationalAgingLab/ComputAge) for convenient operation with datasets and other tools for aging clock design:
131
 
132
  `pip install computage`
@@ -158,6 +160,26 @@ bench = run_benchmark(models_config,
158
  #upon completion, the results will be saved in the folder you specified
159
  ```
160
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
161
  ## Additional Information
162
 
163
  ### Licensing Information
 
127
 
128
  ## Usage Guidelines
129
 
130
+ ### Benchmark a new aging clock
131
+
132
  First install our nice [library](https://github.com/ComputationalAgingLab/ComputAge) for convenient operation with datasets and other tools for aging clock design:
133
 
134
  `pip install computage`
 
160
  #upon completion, the results will be saved in the folder you specified
161
  ```
162
 
163
+ ### Explore the dataset
164
+
165
+ In case you want just to explore our dataset locally, use the following commands for downloading.
166
+ ```python
167
+ from huggingface_hub import snapshot_download
168
+ snapshot_download(
169
+ repo_id='computage/computage_bench',
170
+ repo_type="dataset",
171
+ local_dir='.')
172
+ ```
173
+ Once downloaded, the dataset can be open with `pandas` (or any other `parquet` reader).
174
+ ```python
175
+ import pandas as pd
176
+ #let's choose a study id, for example `GSE100264`
177
+ df = pd.read_parquet('data/computage_bench_data_GSE100264.parquet').T
178
+ #note we transpose data for more convenient perception
179
+ #Don't forget to explore metadata (which is common for all datasets):
180
+ meta = pd.read_csv('computage_bench_meta.tsv', sep='\t', index_col=0)
181
+ ```
182
+
183
  ## Additional Information
184
 
185
  ### Licensing Information