Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-28T11:25:30.517Z
Answers.Text: 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.
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-28T11:58:38.903Z
Answers.Text: I added the possible reason
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-28T07:32:26.007Z
Answers.LastActivityDate: 2018-08-28T11:53:31.180Z
Answers.LastEditDate: 2018-08-28T11:53:31.180Z
Answers.UserDisplayName: Zizogolu
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-24T16:39:10.683Z
Comments.Text: The error message says that you should remove the num.nn, method and do.jaccard argument. Did you try it?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T09:53:07.920Z
Comments.Text: Thank you, yes I removed all except for my URD object but the error is permanent :(
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T09:57:14.363Z
Comments.Text: Can you post the new command and the errors? Could you add the 'print(object)' result?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T10:17:48.940Z
Comments.Text: Please [edit] the question to add the code (in code formatting) . It seems like the error is different now. I'll research a bit
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T10:48:25.067Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T10:57:12.840Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T11:30:43.423Z
Comments.Text: Thank you I also posted in GitHub but URD package developers did to reply
Comments.UserDisplayName: Zizogolu
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T11:45:42.737Z
Comments.Text: 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.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-25T11:55:52.110Z
Comments.Text: definitely you are alright, I am also thankful for your time
Comments.UserDisplayName: Zizogolu
Tags: <r><scrnaseq>
Title: A strange error while clustering of single cell RNA-seq using URD package
ThreadText: # 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  
  
  ---
  
  