Comments (2)
Dear Jing,
Here are five options I can think of when you do not have a full grid of mark/tissue types:
-
Run a stacked model.
-
Run a concatenated model restricting to a subset of stages and/or marks where you have a full grid and then run a concatenated model.
-
Run a concatenated model but treating as missing datasets for which you do not have data ('2' encoding in ChromHMM).
-
Run a concatenated model using impute data from a method such as ChromImpute where you have missing observed data.
-
Run independent models for each stage.
Option 1 has the advantage of using all the data directly and can highly different dynamic patterns so could be a good place to start, but does not provide per-stage annotations if that is what you are interested.
Option 2 has the advantage of being straightforward and allowing well controlled per-stage comparisons but the disadvantage of not using all the data
Option 3 relative to Option 2 uses more data but state usage comparisons will be confounded by the marks available in the stage
Option 4 relative to Option 2 uses more data and relative to Option 3 will be less confounded by the available marks at a stage, but if you have limited data for imputation it might not capture some of the stage specific differences you are interested in capturing
Option 5 is fine if you are interested in studying each stage independently but since you have different state definitions for each stage, stage comparisons are confounded
from chromhmm.
I see. Thank you very much for your very detailed explanations!
from chromhmm.
Related Issues (20)
- discrepancy between X_Y_overlap.png and X_Y_overlap.txt HOT 2
- nullpointerexception error while running CompareModels HOT 2
- Exception` in thread "main" java.util.zip.ZipException: invalid distance too far back HOT 4
- Exception in thread "main" java.lang.UnsatisfiedLinkError: HOT 7
- output truncates chromosomes HOT 4
- WGBS binarization HOT 3
- Binarized data HOT 2
- Coverage as Learnmodel input feature HOT 7
- ConvertGeneTable: Exception in thread "main" java.lang.IllegalArgumentException: invalid strand HOT 4
- Error when using ConvertGeneTable function HOT 3
- model_N.txt file clarification HOT 1
- OverlapEnrichment in LearnModel and standalone gives different results HOT 2
- Only the first 10% of the contigs outputted HOT 2
- chromHMM input choice and annotation of external bed file HOT 1
- Base from OverlapEnrichment command HOT 4
- Reorder genomic annotations and TSS neighborhood HOT 2
- Abnormal annotation at the end of some chromosomes when using LearnModel command HOT 2
- On this data the INFORMATION initialization strategy can only support 4 states HOT 9
- NeighborhoodEnrichment error HOT 2
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 chromhmm.