Comments (1)
Hi @gianasco
At some point last year the model for clonealign changed from using a negative binomial likelihood to multinomial, for speed amongst other things. As a consequence of that, the "size factors" are now just the total reads per cell for each cell. So in a way they are "infer" by default -- I will update the documentation to reflect this.
Kieran
from clonealign.
Related Issues (14)
- Handle situation when copy number is 0
- Add test_that for gradient checking
- Different runs upon the same input generated different results HOT 4
- Initial elbo is NA HOT 7
- How to quantify the clonal frequency consistency between DNA and CloneAlign? HOT 2
- Remove outlying genes now multinomial likelihood is used
- Solve the problem in installing clonealign HOT 1
- row dimensionality issue HOT 2
- Performance with multinomial likelihood HOT 9
- module 'tensorflow' has no attribute 'reset_default_graph' HOT 4
- delta-CN and delta-RNA HOT 1
- the inference runs through one ELBO computation and throws an error (below) if rownames(L) and colnames(Y) don't match or are both NULL.
- when colnames(L) get named in case they are NULL with colnames(Y) <- paste0("gene_", letters[seq_len(ncol(Y))]) wouldn't that give gene_NA if there are more than 26 genes?
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from clonealign.