Issue with running "Basic usage" example

[paula-tataru]

Hi,

I have just installed CellAssign and wanted to try out one of the examples before going on to my own data. I tried the "Basic usage" example from Introduction to CellAssign

Here is my script

library(SingleCellExperiment)
library(cellassign)

data(example_sce)
cat("---------------------\n\nExample single cell experiment\n")
print(example_sce)

cat("---------------------\n\nExample single cell experiment; group\n")
print(head(example_sce$Group))

data(example_marker_mat)
cat("---------------------\n\nExample marker data\n")
print(example_marker_mat)

s <- sizeFactors(example_sce)
fit <- cellassign(exprs_obj = example_sce[rownames(example_marker_mat),], 
                  marker_gene_info = example_marker_mat, 
                  s = s, 
                  learning_rate = 1e-2, 
                  shrinkage = TRUE,
                  verbose = FALSE)
print(fit)
print(head(celltypes(fit)))
print(str(mleparams(fit)))

First of all, it failed loading the example_marker_mat data. I ran with verbose=TRUE and this was part of the output:

name=example_marker_mat:         NOT found in names() of Rdata.rds, i.e.,
        example_TME_markers,example_cellassign_fit,example_rho,example_sce,holik_data

so it looks like the marker example data is missing from the package.

I downloaded it from git and then the script failed with another error:

Error in SummarizedExperiment:::.SummarizedExperiment.charbound(subset,  :
  index out of bounds: Gene1 Gene2 ... Gene9 Gene10
Calls: cellassign ... is -> [ -> [ -> .convert_subset_index -> <Anonymous>

I installed CellAssign using conda.

Any help would be greatly appreciated.

Thanks. Paula Tataru