From d3d20c0af8f83123f22b50f92e2f030e47f9a396 Mon Sep 17 00:00:00 2001 From: Lucas Camillo Date: Sun, 28 Jan 2024 11:25:38 +0000 Subject: [PATCH] Updated todo list --- README.md | 2 +- clocks/notebooks/dnamfitage.ipynb | 5 +++-- docs/_static/clock_glossary.csv | 5 +++-- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 7fdf9fd..ca82d76 100644 --- 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 index 6321d71..a16130e 100644 --- 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 index a483a14..dbff83e 100644 --- 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,,,,