Updated todo list

rsinghlab · Jan 28, 2024 · d3d20c0 · d3d20c0
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -51,7 +51,7 @@ To cite `pyaging`, please use the following:
 
 - [X] Incorporate more murine DNA methylation clocks
 - [X] Add torch data loader for age prediction of large datasets
-- [ ] Move preprocessing/postprocessing step to the AnnLoader 
+- [X] Move preprocessing/postprocessing step to the AnnLoader 
 - [ ] Add other blood chemistry biological age clocks (KD age)
 - [ ] Incorporate proteomic clocks (and datasets)
 - [ ] Integrate scAge clocks (this is proving to be difficult)

diff --git a/clocks/notebooks/dnamfitage.ipynb b/clocks/notebooks/dnamfitage.ipynb
@@ -186,7 +186,7 @@
     "model.metadata[\"approved_by_author\"] = '⌛'\n",
     "model.metadata[\"citation\"] = \"McGreevy, Kristen M., et al. \\\"DNAmFitAge: biological age indicator incorporating physical fitness.\\\" Aging (Albany NY) 15.10 (2023): 3904.\"\n",
     "model.metadata[\"doi\"] = 'https://doi.org/10.18632/aging.204538'\n",
-    "model.metadata[\"notes\"] = None"
+    "model.metadata[\"notes\"] = 'Reference values is mean between male and female training medians'"
    ]
   },
   {
@@ -526,7 +526,7 @@
       " 'clock_name': 'dnamfitage',\n",
       " 'data_type': 'methylation',\n",
       " 'doi': 'https://doi.org/10.18632/aging.204538',\n",
-      " 'notes': None,\n",
+      " 'notes': 'Reference values is mean between male and female training medians',\n",
       " 'species': 'Homo sapiens',\n",
       " 'version': None,\n",
       " 'year': 2023}\n",
@@ -684,6 +684,7 @@
       "Deleted file: Gait_noAge_Males.csv\n",
       "Deleted folder: DNAmFitAge\n",
       "Deleted file: download.r\n",
+      "Deleted folder: .ipynb_checkpoints\n",
       "Deleted file: FemaleMedians.csv\n",
       "Deleted file: MaleMedians.csv\n"
      ]

diff --git a/docs/_static/clock_glossary.csv b/docs/_static/clock_glossary.csv
@@ -14,6 +14,7 @@ leecontrol,methylation,Homo sapiens,2019,✅,https://doi.org/10.18632/aging.1020
 leerefinedrobust,methylation,Homo sapiens,2019,✅,https://doi.org/10.18632/aging.102049,,,,
 leerobust,methylation,Homo sapiens,2019,✅,https://doi.org/10.18632/aging.102049,,,,
 thompson,methylation,Mus musculus,2018,✅,https://doi.org/10.18632/aging.101590,,,,
+dnamfitage,methylation,Homo sapiens,2023,⌛,https://doi.org/10.18632/aging.204538,,,,True
 dnamphenoage,methylation,Homo sapiens,2018,⌛,https://doi.org/10.18632%2Faging.101414,,,,
 dnamtl,methylation,Homo sapiens,2019,⌛,https://doi.org/10.18632/aging.102173,,,,
 dunedinpace,methylation,Homo sapiens,2022,⌛,https://doi.org/10.7554/eLife.73420,The automatic failure if fewer than 80% of the CpG probes are available is not implemented and left to the user's discretion.,quantile_normalization_with_gold_standard,,True
@@ -53,6 +54,6 @@ stubbs,methylation,Mus musculus,2017,⌛,https://doi.org/10.1186/s13059-017-1203
 yingadaptage,methylation,Homo sapiens,2024,⌛,https://doi.org/10.1038/s43587-023-00557-0,,,,
 yingcausage,methylation,Homo sapiens,2024,⌛,https://doi.org/10.1038/s43587-023-00557-0,,,,
 yingdamage,methylation,Homo sapiens,2024,⌛,https://doi.org/10.1038/s43587-023-00557-0,,,,
-zhangblup,methylation,Homo sapiens,2023,⌛,doi,,scale_row,,True
-zhangen,methylation,Homo sapiens,2023,⌛,doi,,scale_row,,True
+zhangblup,methylation,Homo sapiens,2019,⌛,https://doi.org/10.1186/s13073-019-0667-1,,scale_row,,True
+zhangen,methylation,Homo sapiens,2019,⌛,https://doi.org/10.1186/s13073-019-0667-1,,scale_row,,True
 zhangmortality,methylation,Homo sapiens,2019,⌛,https://doi.org/10.1038/ncomms14617,,,,