Error when calculating significance using lo$calculateSignificanceLevel(100)

[ArashDepp007]

Dear @konsolerr, Your tool is giving some good results but, I am getting an error when trying to calculate the significance of correlations using the lo$calculateSignificanceLevel(100) function. My input data consisted of TPM values for 8000 genes and 1000 samples, to which I ran the following commands:

lo <- LinseedObject$new(a, topGenes = 5000); lo$calculatePairwiseLinearity(); lo$calculateSpearmanCorrelation(); lo$calculateSignificanceLevel(100); However the last command raises the following error

Error in sparseMatrix(i = ij[, 1], j = ij[, 2], x = values, dims = c(genes, : length(x) must not exceed length(i)

I tried to do some debugging, and identified the problematic part of the code

ij <- which(upper.tri(self$pairwise) & self$pairwise > 0 & self$spearman > spearmanThreshold, arr.ind = T)

values <- self$pairwise[upper.tri(self$pairwise) & self$pairwise > 0 & self$spearman > spearmanThreshold] * self$spearman[upper.tri(self$pairwise) & self$pairwise > 0 & self$spearman > spearmanThreshold]

genes <- nrow(self$pairwise) edges <- length(values)

So in this section of code, for my data, the variable ij is a matrix of indices with 163623 rows and 2 columns. However, the variable named as values contained 163630 values. Therefore, in next step, when trying to create a sparse matrix with the following code

sparsePP <- sparseMatrix(i = ij[, 1], j = ij[, 2], x = values, dims=c(genes, genes))

It raises an error saying Error in sparseMatrix(i = ij[, 1], j = ij[, 2], x = values, dims = c(genes, : length(x) must not exceed length(i)

I believe this results from the facts that there is mismatch between the dimensions of ij and length of variable values. Could you please take a look and help me trouble shoot it?