PRECAST IntegrateSpaData errors · Issue #2 · feiyoung/PRECAST (original) (raw)

Hello, when I try to run the package I encounter the following two errors:

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': Cannot find 'RNA' in this Seurat object

This stems from line 9 of IntegrateSpaData:
XList <- lapply(PRECASTObj@seulist, function(x) Matrix::t(x[["RNA"]]@DaTa))

Is the intention of this line to use the normalized or non-normalized assay of the Seurat object? (E.g., Spatial or SCT)

If I fix this error by copying one of the existing assays (Spatial or SCT) to an assay named "RNA", I experience another error.

Error in intersect((genelist), Mouse_HK_genes$Gene) :
object 'Mouse_HK_genes' not found

This stems from line 24 of IntegrateSpaData:
houseKeep <- switch(lower_species, human = {
intersect((genelist), Mouse_HK_genes$Gene)

The script is trying to reach for the mouse gene list that wasn't defined. What is the exact purpose of this list?