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Error in GraphClustering function

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
• 1,953 views • link
written by Za Za

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.

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

1 answer

what happens if you try:

object <- URD::graphClustering(object, num.nn = c(5,8,10,15), method="Louvain", do.jaccard = TRUE)
• 1 views • link
written by h.mon h.mon

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

• 1 views • link
written by Za Za

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

Thank you again

• 1 views • link
written by Za Za

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.

• 1 views • link
written by h.mon h.mon

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