Comments (3)
I have a similar issue so I post here and add a comment: in principle, I think you can modify the package to use find_dmrs()
on something different from flow.Sorted.Blood450k
. I am currently trying to achieve that since I don't think this will violate any key assumption of the work. In your case, you would need to add at least the hepatocyte profiles, since you expect your biopsies to contain liver cells + other stuff. The TCGA data should be suitable to call those DMRs, but adapting the code is not straight forward and only the authors can tell us if that is correct. In any case, I think that more plasticity at the level of DMR selection would really broaden the application of this package.
from methylcc.
Thanks @Niinleslie @GMFranceschini for opening the issue. Add another request to this thread too (https://support.bioconductor.org/p/132689/#132691).
There seems to be a sufficient enough interest in making this flexible for other types of cell types besides whole blood. This summer I do not have time to make those changes to the software, but I'm happy to work these ideas this fall.
Thanks for your interest in the package and I appreciate your patience. I will leave the issue open for now as a reminder to get back to this asap.
from methylcc.
Related Issues (5)
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 methylcc.