Error in GraphClustering function

Question

[Za]

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"’

[Jean-Karim Heriche]

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.

Answer 1

[h.mon]

what happens if you try:

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

[Za]

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

[Za]

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

Thank you again

[h.mon]

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.