illuminahumanmethylationepicv2manifest's People
illuminahumanmethylationepicv2manifest's Issues
mapToGenome not working with EPIC v2
Hello,
I am able to get a methyl set and ratio set. But whenever I run mapToGenome
the genomic ratio set or genomic methyl set are empty. I am using the new EPIC v2 manifest and IlluminaHumanMethylationEPICv2anno.20a1.hg38 annotation.
Also, the estimateCellCounts does not seem to work with the new array.
Thanks.
EPIC V2 Conumee
Hi, I used IlluminaHumanMethylationEPICv2manifest and minfi to get the Mset.
When trying to use Conumee, also the version from mwsill, I am running into this error when trying to create an annotation object:
using genome annotations from UCSC Loading required package: IlluminaHumanMethylationEPICv2anno.ilm10b4.hg19 Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'sort': cannot load annotation package IlluminaHumanMethylationEPICv2anno.ilm10b4.hg19
Can someone help me with this issue? Thanks!
Annotation package
Dear Martin,
Many thanks for providing this manifest. Are there any plans to create a separate annotation package for EPICv2? The reason I ask is that attempting to normalise with any other method in minfi returns an error, due to the lack of an accompanying IlluminaMethylationAnnotation object required by preprocessFunnorm() and other normalisation methods. Understanding the requirements and structure of the various minfi objects is a trial for me at the best of times, so thank you for getting the ball rolling.
Best,
Tim
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ 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. ๐๐๐
-
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 โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.