Error in restrictCorpus() in default settings.

[lelandwilliams]

Following the blog post "10x Visium spatial transcriptomics data analysis with STdeconvolve in R" with my own data, I created gexp2.

This code fails:

> corpus <- restrictCorpus(gexp2)
Removing 2 genes present in 100% or more of pixels...
18083 genes remaining...
Removing 6422 genes present in 5% or less of pixels...
11661 genes remaining...
Restricting to overdispersed genes with alpha = 0.05...
Calculating variance fit ...
Using gam with k=5...
1272 overdispersed genes ... 
 Using top 1000 overdispersed genes.

Error in .subscript.2ary(x, i, , drop = TRUE) : subscript out of bounds

But when I set nTopOD, it succeeds:

> corpus <- restrictCorpus(gexp2, nTopOD = NA)
Removing 2 genes present in 100% or more of pixels...
18083 genes remaining...
Removing 6422 genes present in 5% or less of pixels...
11661 genes remaining...
Restricting to overdispersed genes with alpha = 0.05...
Calculating variance fit ...
Using gam with k=5...
1272 overdispersed genes ... 
Genes in corpus > 1000 (1272). This may cause model fitting to take a while. Consider reducing the number of genes.