Comments (2)
Hi Roman,
Thanks for trying out HoneyBADGER!
I believe the error is due to the data being from mouse. A number of default options have been set under the assumption that the data is from human. For example, hb$setGexpMats
has an id
parameter that is by default 'hgnc_symbol'.
You will want to specify 'mgi_symbol' in your case assuming that the rownames in your matrix.sample
are indeed MGI symbols. You can specify other biomaRt identifiers if your rownames are ENSEMBL or something else:
hb$setGexpMats(matrix.sample, matrix.ref, mart.obj,
filter=FALSE, scale=FALSE, verbose=TRUE, id='mgi_symbol')
setGexpMat
then uses this id
and your mart.obj
to map genes to their genomic positions in the chromosome. You can double check that this is being done properly by looking at hb@gene
; it should contain a GenomicRanges representation of genomic positions for all your genes.
Now, hb$plotGexpProfile()
should be able to organize the genes by their genomic positions and make the appropriate visualization.
You can learn more about each function using and their default parameters:
?setGexpMats
Let me know if this fixes the issue.
Best,
Jean
from honeybadger.
That worked, thanks a lot! I guess I should've checked the additional parameters :)
from honeybadger.
Related Issues (20)
- lt$setGexpDev HOT 1
- Warning in setGeneFactors and error in retestIdentifiedCnvs
- Allele-mode for selecting normal cells HOT 2
- 10X + Honeybadger question HOT 2
- Error in summarizeResults HOT 3
- Error in calcGexpCnvBoundaries when running with numeric chromosome names HOT 1
- Error: subscript contains invalid names HOT 9
- read bam files HOT 4
- Filtering of identified CNVs HOT 2
- speed of running setAlleleMats step
- What is the reason for only including snps in HoneyBADGER? HOT 2
- gene filtering different in HoneyBADGER object HOT 3
- Error: Failed to install 'HoneyBADGER' from GitHub HOT 2
- Showing error when trying Getting_Started.Rmd
- no method for coercing this S4 class to a vector HOT 3
- showing NULL in the step of calcGexpCnvBoundaries - getting started tutorial HOT 12
- Applying bayesian hierarchical model in integrating analyses tutorial
- error in hb$summarizeResults
- Error in summarizeResults for the allele-based approach
- Error in calcCombCnvProb 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 honeybadger.