Question: Error in GraphClustering function
0
gravatar for Za
7 months ago by
Za120
Za120 wrote:

Hi,

Long time I am trying this tutorial

https://github.com/farrellja/URD/blob/master/Analyses/QuickStart/URD-QuickStart-AxialMesoderm.md

On sample data provided in tutorial no error but with my own data I am always being stopped with this error. Who could help me to solve that please?

> 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) 
URD object: 12451 genes x 1556 cells. 


object <- graphClustering(object) 
Show Traceback Rerun with Debug Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘graphClustering’ for signature ‘"URD"’
R • 261 views
ADD COMMENTlink written 7 months ago by Za120
1

The unused argument error often shows up when you have two functions with the same name but using different arguments. Check that you haven't redefined the graphClustering() function somewhere.

ADD REPLYlink written 7 months ago by Jean-Karim Heriche18k
3
gravatar for h.mon
7 months ago by
h.mon24k
Brazil
h.mon24k wrote:

what happens if you try:

object <- URD::graphClustering(object, num.nn = c(5,8,10,15), method="Louvain", do.jaccard = TRUE)
ADD COMMENTlink written 7 months ago by h.mon24k

Thanks a lot, after long time worked. I two times emailed the developers but finally you solved that

> object <- URD::graphClustering(axial.6somite, num.nn = c(5,8,10,15), method="Louvain", do.jaccard = TRUE)
>

Thank you so much once again

ADD REPLYlink modified 7 months ago • written 7 months ago by Za120

Excuse me, could you please tell me how URD:: solved the error?

Thank you again

ADD REPLYlink written 7 months ago by Za120
1

You are telling R to use the graphClustering() function from the URD namespace. You probably loaded another package with a different graphClustering() function - or defined one yourself - which is taking precedence over URD's function.

ADD REPLYlink written 7 months ago by h.mon24k
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