I am using the hypergraph package specifically because I want to try hypergraph partitioning on some pairwise data I have.
I've populated my hypergraph by creating hyperedges for each of my sample names that meet a pairwise threshold criteria with other sample names. For example: is sampleA shares a pairwise value of between 0.4 and 0.6 with sampleB and sample_C, then all three are described by a hyperedge.
But when I use the kCoresHypergraph() function to partition my hypergraph into cores, I get this error:
> kCoresHypergraph(STX_hypergraph) **Error in im[r_chosen, c_chosen] : subscript out of bounds.**
After digging a bit deeper this appears to be a bug.
> options(error=recover) > STX_cores <- kCoresHypergraph(STX_hypergraph) **Error in im[r_chosen, c_chosen] : subscript out of bounds** >Enter a frame number, or 0 to exit >1: kCoresHypergraph(STX_hypergraph) >2: matrix(im[r_chosen, c_chosen], nrow = length(r_chosen), ncol = length(c_cho >Selection: 2 >Called from: top level >Browse> ls()  "byrow" "data" "dimnames" "ncol" "nrow" >Browse> data **Error during wrapup: promise already under evaluation: recursive default argument reference or earlier problems?** > Browse> dim(im)  170 21 > Browse> r_chosen 91633 185314 84 167 > Browse> c_chosen  35 36
It is also worth mentioning that my constructed hypergraph does not throw an error with the vCoverHypergraph() function. Therefore, there must be something awry with the kCoresHypergraph() function.
If somebody could help me with this I would greatly appreciate it.