[R] help with package ranks

[Jim Lemon]

Hi Davide,
The error message is probably due to a zero length dimension in:

W[,ind.positives]

I would look at W (data frame?) to see where this might occur. That
is, does W have a set of proteins with _no_ annotations? Perhaps
manually removing that set will get the function running.

Jim


On Wed, Apr 5, 2017 at 5:14 AM, davide f <samantha.fundetta at gmail.com> wrote:
> Hello, I'm Davide.
> I'm using the package RANKS, in particular the functions do.GBA, do.RW,
> do.RANKS. To the funcs are given 2 different Matrix. One is a a simmetryc
> adjacency Matrix(called "M"), where rows and columns are protein, and the
> other is an annotation Matrix(called "ann"), where protein are rows(the
> same of the first Matrix) and and the annotations are columns.
>
> I write a script in order to filter both the matrices, choosing only
> protein with 5 or more annotations.
>
> To be more specific, using the functions, data=M, labels=ann.
>
> But, running the script, it gives me an error message about the functions
> of interest:
>
> Error in apply(W[, ind.positives], 1, sum) :
>   dim(X) deve avere lunghezza positiva
>
>
> In paritcular it gives me the error during the FOR cycle, when it
> works on the 6th column.
>
>
> How can I resolve it? what is the reason?
>
>
> Thank you in advance, best regards,
>
> Davide.
>
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