Open soheilj opened 10 months ago
That's a great catch!
We just made a new release of rliger package 2.0. And we are abandoning the seurat wrappers since we allowed the native Seurat object support in the new version. I.e. you can directly call a rliger function using a Seurat object now. The rliger wrapper functions in SeuratWrappers package is not yet updated accordingly but we are planning on deprecating them.
For the specific point you're making, I'm very sure that now the feature names come directly from the scaled matrix objects. And it doesn't matter if you use a Seurat or liger object.
Yichen
Hi,
I think the following part in the
RunOptimizeALS()
SeuratWrapper function has potentially a bug.Fetching the scaled data matrix from the Seurat object without specifying the gene order would not necessarily have the same order of genes as appears in the
VariableFeatures()
function. So in the last line, gene names can be assigned to column names of theout$W
matrix in an incorrect order.I think adding the gene order after the
GetAssayData()
would be an easy fix.