Error when simulating more samples with splatPop

[wanghao98]

Hi, in the tutorial, samples = 5 was used to simulate data. When I tried to increase sample size to more than 20, I had the following error:

Error in sample.int(length(x), size, replace, prob) : invalid first argument

Here is the Code I used:

vcf = mockVCF(n.sample = 40)
gff <- mockGFF()

params.cond <- newSplatPopParams(eqtl.n = 0.5, 
                                 batchCells = 100,
                                 similarity.scale = 5,
                                 condition.prob = c(0.5, 0.5),
                                 eqtl.condition.specific = 0.5,
                                 cde.facLoc = c(0.5, 0.5), 
                                 cde.facScale = c(0.5, 0.5))
sim.pop.cond <- splatPopSimulate(vcf = vcf, gff = gff, params = params.cond, 
                                 sparsify = FALSE)

Thank you for looking into this!

[azodichr]

Thanks for bringing this to our attention @wanghao98! I've looked into the problem and found a minor code bug that was causing it. I have pushed the fix to @lazappi to review and once accepted you should be able to install the updated package from github. Let us know if you have any more trouble with splatPop!

[lazappi]

@wanghao98 This should be fixed now and will be in the current Bioconductor release (3.14) and devel (3.15) soon. If you haven't updated to the new Bioconductor version yet you can install it from GitHub.