I'm having an issue with the network generated via the correlationTest function in metagenomeSeq. The final edge of the network seems to be missing; that is, I attempted to generate a co-abundance network using a subset of the 800 most variable OTUs from msd16s data, which should generate a network of 319600 edges. This is the size of the network generated, but edge 319600 is not listed (it should be an edge between OTU # 477 and 856).
I appreciate your attention to this apparent bug.
Here is the code that I used to generate my network:
dat <- msd16s
cases <- which(pDat$Type == "Case")
counts <- log(MRcounts(dat)+1,base = 2)
vars <- apply(counts,MARGIN = 1,var)
ords <- order(vars[1:800],decreasing=T)
Network <- correlationTest(obj = counts[ords,cases],method = "spearman",cores = 2)