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const-ae / transformGamPoi

Variance stabilizing transformation for Gamma Poisson distributed data
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estimate_size_factors with poscounts fails for dgCMatrix #3

Open ChristophH opened 2 years ago

ChristophH commented 2 years ago

Hi Constantin, since there is no colMedians() method for dgeMatrix objects, I get the following error from MatrixGenerics

Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : 
  Failed to find a colMedians() method for dgeMatrix objects.

Casting to matrix somewhere around https://github.com/const-ae/transformGamPoi/blob/d408b11e728fa44805a52ad9aa059b54f6b195a4/R/helpers.R#L126-L131 should fix the issue.

Best, Christoph

Reproducible example:

set.seed(42)
counts <- scales::squish(x = rpois(n = 200, lambda = 3) - 3, range = c(0, Inf))
counts <- Matrix::Matrix(data = counts, nrow = 10, ncol = 20)
sf <- transformGamPoi:::estimate_size_factors(Y = counts, method = 'poscounts')
const-ae commented 2 years ago

Hi Christoph,

thanks for the report. Yes, you are right, adding an as.matrix() somewhere should fix the issue. However, the deeper issue is that MatrixGenerics apparently doesn't yet realize that it should treat dgeMatrix objects as matrix objects, which would be the more elegant solution. I will try and see if I can fix the problem :)