Error with knnImputer from the DMwR Package: invalid 'times' argument

user_6112228 0
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I'm trying to run knnImputer from the DMwR package on a genomic dataset. The dataset has two columns - one for location on a chromosome (numeric, an integer) and one for methylation values (also numeric, double), with many of the methylation values are missing. The idea is that distance should be based on location in the chromosome. I also have several other features, but chose to not include those). When I run the following line however, I get an error.

reg.knn <- knnImputation(as.matrix(testp), k=2, meth="median")
#ERROR:
#Error in rep(1, ncol(dist)) : nvalid 'times' argument

Any thoughts on what could be causing this? If this doesn't work, does anyone know of anything other good KNN Imputers in R packages? I've been trying several but each returns some kind of error.

r
3 Answers

Today, I encountered the same error. My df was much larger than 3 columns, so this seems to be not the (only?) problem.

I found that rows with too much NAs caused the problem (in my case, more than 95% of a given row was NA). Filtering out this row solved the problem.

Take home message: do not only filter for NAs over the columns (which I did), but also check the rows (it's of course impossible to impute by kNN if you cannot define what exactly is a nearest neighbor).

Would be nice if the package would provide a readable error message!

user_121481440

When I read into the code, I located the problem, if the column is smaller than 3, then in the process it where down-grade to something which is not a dataframe and thus the operation based on dataframe structure all fails, I think the author should handle this case.

And yes, the last answer also find it by trial, different road, same answer

user_31796980
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