<p>This solved the error</p>

<pre><code>object &lt;- URD::graphClustering(object) 
</code></pre>

<p><strong><em>By this function I am telling R to use the graphClustering() function from the URD namespace. I probably had loaded another package with a different graphClustering() function - or defined one myself - which is taking precedence over URD's function.</em></strong></p>

CC BY-SA 4.0
2018-08-28T11:25:30.517Z
It's nice that you have shared a solution to your problem. But since it was not very clear what is the actual problem, this answer is not really explaining anything.
Kamil S Jaron
CC BY-SA 4.0
2018-08-28T11:58:38.903Z
I added the possible reason
Zizogolu
CC BY-SA 4.0
2018-08-28T07:32:26.007Z
2018-08-28T11:53:31.180Z
2018-08-28T11:53:31.180Z
Zizogolu
<p>I am using URD R package on my single cell RNA-seq data hoping to be able to trace gene expression changes during the development. After dimension reduction step by PCA and diffusion map whatever I am trying to cluster some cells, but whatever I do I am getting this error </p>

<pre><code>&gt; object &lt;- graphClustering(object, num.nn = c(5,8,10,15), method="Louvain", do.jaccard = TRUE)
Error in graphClustering(object, num.nn = c(5, 8, 10, 15), method = "Louvain",  : 
  unused arguments (num.nn = c(5, 8, 10, 15), method = "Louvain", do.jaccard = TRUE)


&gt; print(object.6s) 
URD object: 12451 genes x 1556 cells. 


object.6s.mnn &lt;- graphClustering(object.6s) 
Show Traceback Rerun with Debug Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘graphClustering’ for signature ‘"URD"’
</code></pre>

<p>I tried to change Louvain, jaccard, ... but I am still getting this error. How can I get rid of it?</p>

CC BY-SA 4.0
2018-08-24T16:39:10.683Z
The error message says that you should remove the num.nn, method and do.jaccard argument. Did you try it?
llrs
CC BY-SA 4.0
2018-08-25T09:53:07.920Z
Thank you, yes I removed all except for my URD object but the error is permanent :(
Zizogolu
CC BY-SA 4.0
2018-08-25T09:57:14.363Z
Can you post the new command and the errors? Could you add the 'print(object)' result?
llrs
CC BY-SA 4.0
2018-08-25T10:17:48.940Z
Please [edit] the question to add the code (in code formatting) . It seems like the error is different now. I'll research a bit
llrs
CC BY-SA 4.0
2018-08-25T10:48:25.067Z
The problem is they define a new class but they don't define methods for said class. The package would need (IMHO) more test and add methods for said class. It would be still possible to work with functions if they defined a generic class, but that's beyond what we can answer/solve here, they need to modify the package.
llrs
CC BY-SA 4.0
2018-08-25T10:57:12.840Z
Also, please consider asking to the right people next time. If you post an issue in the package it signals that there is something wrong with the package(you followed the tutorial as you did and you found a problem), while if you post it here I understand that there is some problem while using the package (you are trying to do something not covered by the help file or the tutorial and don't know how to do it). Either way if it is a "simple" informatics error probably Bioinformatics.SE is not the best place to post it.
llrs
CC BY-SA 4.0
2018-08-25T11:30:43.423Z
Thank you I also posted in GitHub but URD package developers did to reply
Zizogolu
CC BY-SA 4.0
2018-08-25T11:45:42.737Z
Yes, I saw, it but don't expect people to answer the emails or questions in 5 minutes. The developers (and people on the forums, here on biostars or in support.bioconductor) have other things to do and are answering you on their own time, because they want to help you. To help you they need to spend some time figuring the error and correcting it for you, so it takes some time to give you an answer. I hope you get your answers and solution to these problem.
llrs
CC BY-SA 4.0
2018-08-25T11:55:52.110Z
definitely you are alright, I am also thankful for your time
Zizogolu
<r><scrnaseq>
A strange error while clustering of single cell RNA-seq using URD package
# A strange error while clustering of single cell RNA-seq using URD package

(Asked by: username_0 on 2018-08-24)

I am using URD R package on my single cell RNA-seq data hoping to be able to trace gene expression changes during the development. After dimension reduction step by PCA and diffusion map whatever I am trying to cluster some cells, but whatever I do I am getting this error 
> object <- graphClustering(object, num.nn = c(5,8,10,15), method="Louvain", do.jaccard = TRUE)
Error in graphClustering(object, num.nn = c(5, 8, 10, 15), method = "Louvain",  : 
  unused arguments (num.nn = c(5, 8, 10, 15), method = "Louvain", do.jaccard = TRUE)


> print(object.6s) 
URD object: 12451 genes x 1556 cells. 


object.6s.mnn <- graphClustering(object.6s) 
Show Traceback Rerun with Debug Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘graphClustering’ for signature ‘"URD"’

I tried to change Louvain, jaccard, ... but I am still getting this error. How can I get rid of it?

**Tags:** r, scrnaseq
> **Comments:**
> **username_1**: The error message says that you should remove the num.nn, method and do.jaccard argument. Did you try it?  
> **username_0**: Thank you, yes I removed all except for my URD object but the error is permanent :(  
> **username_1**: Can you post the new command and the errors? Could you add the 'print(object)' result?  
> **username_1**: Please [edit] the question to add the code (in code formatting) . It seems like the error is different now. I'll research a bit  
> **username_1**: The problem is they define a new class but they don't define methods for said class. The package would need (IMHO) more test and add methods for said class. It would be still possible to work with functions if they defined a generic class, but that's beyond what we can answer/solve here, they need to modify the package.  
> **username_1**: Also, please consider asking to the right people next time. If you post an issue in the package it signals that there is something wrong with the package(you followed the tutorial as you did and you found a problem), while if you post it here I understand that there is some problem while using the package (you are trying to do something not covered by the help file or the tutorial and don't know how to do it). Either way if it is a "simple" informatics error probably Bioinformatics.SE is not the best place to post it.  
> **username_0**: Thank you I also posted in GitHub but URD package developers did to reply  
> **username_1**: Yes, I saw, it but don't expect people to answer the emails or questions in 5 minutes. The developers (and people on the forums, here on biostars or in support.bioconductor) have other things to do and are answering you on their own time, because they want to help you. To help you they need to spend some time figuring the error and correcting it for you, so it takes some time to give you an answer. I hope you get your answers and solution to these problem.  
> **username_0**: definitely you are alright, I am also thankful for your time  

---

## 1 answers

### Answer by username_0 on 2018-08-28. Score: -1 | Accepted answer

This solved the error
object <- URD::graphClustering(object) 

By this function I am telling R to use the graphClustering() function from the URD namespace. I probably had loaded another package with a different graphClustering() function - or defined one myself - which is taking precedence over URD's function.

> **Comments:**
> **username_2**: It's nice that you have shared a solution to your problem. But since it was not very clear what is the actual problem, this answer is not really explaining anything.  
> **username_0**: I added the possible reason  

---

