Comments (5)
Thanks!
Yes you could do that.
But you'd have to implement the extraction of sets of cluster markers from Seurat and conform them to a names list, much like we do with the output of WGCNA. We try to keep hypeR as general as possible, so we do not have plans to add something like this directly into the package.
from hyper.
thank for your reply.
I extracted the ranked gene names from the clusters and run
mhyp_mouse <- hypeR(cluster_markers, gsets, test="hypergeometric", background=30000)
the output are cluster names
0
1
2
3
4
5
6
...
then I run
hyp_dots(mhyp_mouse, merge=TRUE, fdr=0.05, title="cluster") got the error message
Error in hyp_dots(mhyp_mouse, merge = TRUE, fdr = 0.05, title = "cluster"): unused argument (merge = TRUE)
It says, merge not used. When I removed the merge parameter, the dot plots are showing, but between cluster 14 plot and cluster 15, it printed
$0
$1
$2
$3
$4
$5
$6
...
finally, if I run
mhyp_mouse
it shows
(multihyp)
(hyp) 0
50 x 8
(hyp) 1
50 x 8
(hyp) 2
50 x 8
(hyp) 3
50 x 8
(hyp) 4
50 x 8
(hyp) 5
50 x 8
(hyp) 6
50 x 8...
what do you think might cause the error? It can generate the dot plots, but cannot output the results.
this is how I generated wgcna-like input
cluster_markers<- list()
for(i in unique(markers$cluster)) {
cluster_markers[[i]] <- subset(markers$gene, markers$cluster==i)
}
markers is the data frame output from seurat function FindAllMarkers , I just extracted the ranked gene names
| p_val | avg_logFC | pct.1 | pct.2 | p_val_adj | cluster | gene
Ctss | 8.784173e-164 | 2.604368 | 0.992 | 0.129 | 2.207199e-159 | 0 | Ctss
from hyper.
What version of hypeR are you using? The merge
parameter for hyp_dots()
is a relatively new feature.
from hyper.
The latest version
from hyper.
The latest version installed through Github? Can I see your session info?
from hyper.
Related Issues (20)
- GSEA arguement not recognised hypeR HOT 1
- Error in conexion HOT 1
- quiet
- reactable should be "wider" HOT 1
- Enrichment maps unable to export in a .tiff format HOT 2
- Duplicated gene symbols in the output of msigdb_download HOT 6
- sizes argument in hyp_dots function HOT 1
- error in GSEA about weighted signatures HOT 1
- How to get signetures enriched in a pathway? HOT 1
- hypeR-dot plots with KS test should incorporate directionality information
- KS with mx.diff=TRUE (GSVA-like)
- .check_overlap returns a fraction, not a percentage HOT 1
- Error in hyp_hmap HOT 2
- X-axis and Outputting Gene Overlap Size HOT 2
- rctbl_build does not work with method="ks" HOT 1
- .kstest needs to match ks.test (modulo the sign)
- MSigDB C7 retrieval fails
- rgsets does not support proper object "duplication" by value
- Hits names should be quoted (like in the csv format)
- Pushing to upstream on Bioc
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 hyper.