Comments (2)
From a quick view at the code in the methods script, it seems the correlation has to be perfect, but there's also a mention of having a 'softer' mention so I'm not 100% sure 😅
from scoary.
Thanks for your question, and sorry about the wait.
As you have already figured out, the genotypes need to be 100% correlated to be collapsed. You may also have seen from the code that I thought about using a softer threshold, but I have never gotten around to implementing that.
I'm also a bit uncertain how the distribution of the collapsed variant should be counted, i.e. should it be present in all isolates with either of the original variants? I'm uncertain how that would impact other assumptions that are made.
Another thing I'm not sure about is whether the collapsed genes should then go through subsequent rounds of correlation -> collapse. That is, when we collapse two genes into one, this will have a new distribution pattern, and there is a chance that this new pattern will fall within the correlation threshold of being collapsed with yet another gene.
from scoary.
Related Issues (20)
- How can I explore the differences between subpopulations defined using population analysis?
- genetic differences among populations defined by population analysis HOT 2
- How to generate manhatton plot from Scoary results HOT 1
- Stop at "Calculating max number of contrasting pairs for each nominally significant gene: in the Ternimal
- Should assemblies be removed if core gene alignment shows redundancies?
- Unrecognized character found in trait file HOT 2
- UnicodeDecode Error while reading traits file
- Significance of the worst_pairwise_p HOT 3
- missing data in genotype file
- _csv.Error: field larger than field limit (131072)
- IndexError: list index out of range HOT 4
- Gene enrichments across host sites
- /var/spool/gridengine/execd/cu17/job_scripts/371921: line 11: 9884 Killed HOT 1
- I got the CSV files of all trait related genes. How do I get the important genes in all trait files?
- collapse flag output
- Support for non-binary traits HOT 9
- Startcol error HOT 1
- Convert vcf from parsnp to Scoary input
- Large number of significant genes 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 scoary.