Comments (2)
Since the gene centers and loadings are not in the object, the input reducedDim is not available for artificial doublets, and hence it can't be used for the actual training. It is used only for the initial clustering -- unless you input the clusters, in which case it's not used at all. This means that, for this step, you can use your custom space in the following way:
sce$fastclusters <- fastcluster(sce, rdname="myReducedDimName")
sce <- scDblFinder(sce, clusters="fastclusters")
In multi-sample settings, it's anyway advisable to use global clusters and detect doublets separately (the default multiSampleMode): this is more robust to technical variation and, unless you have very few cells, the classifier wouldn't anyway gain much from the additional samples.
If you wanted to use a different space for the downstream steps (i.e. also on artificial doublets) as well, you can pass a custom function to the processing
argument.
from scdblfinder.
Useful thanks.
I will close
from scdblfinder.
Related Issues (20)
- Issue with knownDoublets HOT 3
- Forgot to import sweep from DelayedArray HOT 3
- BiocParallel error - could not find symbol 'useNames' in environment of the generic function HOT 2
- Issue running scDblFinder on scATAC-seq data HOT 3
- Exploring Overrepresented Doublets HOT 3
- scDblFinder not deterministic when using batch+BPPARAM HOT 9
- xcgboost install HOT 2
- size factors should be positive in computeDoubletDensity HOT 1
- why error ? HOT 4
- Possible Bug: cxds2 call does not include artificial doublets in whichDbls HOT 1
- V minor coding bug with multiSampleMode = 'split' and returnType = 'table'
- Running scDblFinder deterministic and serial with the 'samples' parameter HOT 3
- Error in installing scDblFinder: object ‘colBlockApply’ is not exported by 'namespace:beachmat' HOT 5
- How to find all features used in training HOT 1
- Doublet numbers still not reproduced even though I used BPPARAM and bpstart HOT 2
- Deprecated "dgcMatrix" HOT 2
- scDbliFinder.sample is different from the sample column specified in `scDblFinder` function `samples` column ? HOT 17
- doublets mostly differ between scDblFinder and doubletFinder HOT 18
- Merging multiple samples with scATAC prior to scDblFinder 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 scdblfinder.