Comments (6)
Hey! The problem is this line: eng.get_charge_peaks(). When you remove that, I think it will work. What were you hoping to get out of the get_charge_peaks function?
It's meant to convert the charge distribution into a pks object for the sake of making a plot in the GUI. Unfortunately, it writes over the actual mass peaks object, which is what is causing the error. This is partially my lazy coding, but it also makes it easier for users to interact with the charge states like they would mass peaks, which is helpful for some GUI operations.
from unidec.
Thanks a lot! I was trying to test if I can extract the change from the peak. Another problem I'm facing is the DScore, which always returns 0 in my case when using export_params(). Would you know what could cause this?
from unidec.
It should report the average charge state automatically with export_params() (see AvgCharge). It will also write out the _chargedata.dat for the intensities of each charge state for each peak. More info here: https://github.com/michaelmarty/UniDec/wiki/What-Are-All-Those-File-Outputs-and-How-Can-I-Export-My-Data#peak-detection
Let me see if can track down what's happening with the export params and Dscore
from unidec.
Can you describe the DScore issue more? I'm not seeing it when I test simply repeating the export_params in the GUI
from unidec.
It might be an error in the dockerfile. This happens only when using the docker.
Using export_params() with docker terminal:
import unidec
eng=unidec.UniDec()
eng.open_file("BSA.txt", "./unidec_test")
eng.process_data()
eng.run_unidec(silent=True)
eng.pick_peaks()
eng.export_params()
BSA_peakparam.dat:
Mass MassStdGuess AvgCharge StdDevCharge Height Area MassCentroid MassFWHM MassErrorBetweenZ DScore
66420.000000 12.737862 14.985720 0.576081 100.000000 100.000000 66420.070452 24.000000 1.223040 0.000000
Using GUI:
BSA_peakparam.dat:
Mass MassStdGuess AvgCharge StdDevCharge Height Area MassCentroid MassFWHM MassErrorBetweenZ DScore
66211.000000 14.909570 14.909570 0.610480 1.331321 1.271188 66211.556002 25.000000 0.414636 0.914815
(...)
from unidec.
Great! I think I found the problem. The command line doesn't automatically calculate the DScore, unlike the GUI, which runs it as part of the peak picking. Try adding eng.dscore() after the pick_peak() command. I also just added it automatically to the pick_peak function now, and the Docker should be updated to reflect this. Thanks for finding this!
from unidec.
Related Issues (19)
- Bug in Cube Plots HOT 1
- v3.1.0 won't open HOT 1
- pdf generation resulted in fatal error if file name contain . HOT 2
- Import of mzML files for "Using MetaUniDec to Analyze Chromatograms" not working HOT 3
- m/z range HOT 6
- mzML files and Linux HOT 2
- Exporting Waterfall Plot from Meta UniDec 4.2 HOT 2
- Converting data recorded with bunching factor to txt HOT 7
- RNA or DNA deconvolution HOT 1
- Scale problem HOT 2
- trying to create txt input HOT 5
- Could not import data reader: unidectools HOT 1
- Suggestion for MetaUniDec to skip bad runs HOT 2
- error with opening .raw files HOT 5
- Error 3e+09 HOT 7
- Unable To Make TIC Selection HOT 2
- Unable to output the DScore for each deconvoluted mass HOT 2
- mzML files won't open - error HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from unidec.