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proms's Introduction

ProMS: protein marker selection using proteomics or multi-omics data

ProMS (Protein Marker Selection) is a python package designed to tackle a novel problem of multiview feature selection: given multiple views of same set of samples, select important features from one view of interest (target view) by integrating information from other views. It was initially developed to select protein biomarkers using proteomics data with the help of additional omics views (e.g. RNAseq).

Check out the documentation

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proms's Issues

How to run proms program ?

Hi Proms community.

I tried to run proms program, unfortunately I have received an error message explaining me the program is not installed.

I use Ubuntu 18.

I followed the next steps:

florian@computer /tmp> pip install --upgrade proms
Requirement already satisfied: proms in /home/flonflon/.local/lib/python3.9/site-packages (1.0.5)
Collecting proms
  Using cached proms-1.0.5-py3-none-any.whl (25 kB)
  Using cached proms-1.0.4-py3-none-any.whl (20 kB)
Requirement already satisfied: scikit-learn in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (0.24.1)
Requirement already satisfied: numpy in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (1.20.2)
Requirement already satisfied: scikit-survival in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (0.15.0.post0)
Requirement already satisfied: pandas in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (1.2.3)
Requirement already satisfied: scipy in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (1.6.2)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.9/dist-packages (from proms) (3.2.0)
Requirement already satisfied: pyyaml in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (5.4.1)
Requirement already satisfied: xgboost in /home/flonflon/.local/lib/python3.9/site-packages (from proms) (1.4.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/lib/python3/dist-packages (from matplotlib->proms) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/lib/python3/dist-packages (from matplotlib->proms) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /usr/lib/python3/dist-packages (from matplotlib->proms) (2.8.1)
Requirement already satisfied: cycler>=0.10 in /usr/lib/python3/dist-packages (from matplotlib->proms) (0.10.0)
Requirement already satisfied: pytz>=2017.3 in /usr/lib/python3/dist-packages (from pandas->proms) (2021.1)
Requirement already satisfied: joblib>=0.11 in /home/flonflon/.local/lib/python3.9/site-packages (from scikit-learn->proms) (1.0.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/flonflon/.local/lib/python3.9/site-packages (from scikit-learn->proms) (2.1.0)
Requirement already satisfied: ecos in /home/flonflon/.local/lib/python3.9/site-packages (from scikit-survival->proms) (2.0.7.post1)
Requirement already satisfied: numexpr in /home/flonflon/.local/lib/python3.9/site-packages (from scikit-survival->proms) (2.7.3)
Requirement already satisfied: osqp!=0.6.0,!=0.6.1 in /home/flonflon/.local/lib/python3.9/site-packages (from scikit-survival->proms) (0.6.2.post0)
Requirement already satisfied: qdldl in /home/flonflon/.local/lib/python3.9/site-packages (from osqp!=0.6.0,!=0.6.1->scikit-survival->proms) (0.1.5.post0)
florian@computer /tmp> proms_train -h
proms_train: command not found

Do you have any idea to help me to run it ?

Does ProMS support multi-class feature selection?

Thank you for the ProMS. It is really a nice tool for feature selection.
In the data preparation section of the docs,

For binary classification task, the valid label values are either 0 (negative class) or 1 (positive class). For surival analysis task, columns for both event indicator and survival/censoring time should be provided.

I am wondering if ProMS supports multi-class feature selection, i.e., more than two classifications, and how should we prepare the Label data.

Thanks in advance.

Permission error with proms_predict

Hello and thank you for ProMS,
I have successfully used ProMS for marker selection on proteomics data. My problem is that prediction on other datasets always failed because of a permission error of a temp file (.yml).

Any idea/solution to help me solve this problem? Thank you in advance for your help.

C:\WINDOWS\system32>cd C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts
C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts>activate
(env) C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts>proms_train -f run_config_file.yml -d nec.yml
data config file: C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts\nec.yml
processing data ...
prediction type: cls
view: pro
train data target view features length 63
test data target view features length 63
common target view features length 63
number of samples: 90
test sample size: 91
k=22, repeat=1, estimator=lr, fs_method=proms
acc:0.9259, auroc: 0.9725
k=22, repeat=2, estimator=lr, fs_method=proms
acc:0.8889, auroc: 0.9286
………
k=22, repeat=1, estimator=lr, fs_method=proms
acc:0.967, auroc:0.984

Everything is ok until this step
(env) C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts>proms_predict -m results\2022_09_06_22_15_09\full_model\full_model.pkl -d Prediction_data\FreeSearch_1089entrees_reportpg2.tsv
Traceback (most recent call last):
File "C:\Users\gagd2502\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "C:\Users\gagd2502\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\gagd2502\Desktop\DIAnn\Proms\env\Scripts\proms_predict.exe_main.py", line 9, in
File "c:\users\gagd2502\desktop\diann\proms\env\lib\site-packages\proms\predict.py", line 134, in main
with open(temp.name, 'w') as fh:
PermissionError: [Errno 13] Permission denied: 'C:\Users\gagd2502\AppData\Local\Temp\tmp_8vlaezi.yml'

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