Calling scone with run=TRUE Error
Opened this issue · 1 comments
Maybe I'm missing some obvious point but whenever I try to run sample code:
my_scone <- scone(my_scone,
scaling=scaling,
run=TRUE,
eval_kclust = 2:6,stratified_pam = TRUE,
return_norm = "in_memory",
zero = "postadjust")
I get the following error:
Error in imputation[[im_params[i]]](assay(x), impute_args) :
attempt to apply non-function
I had the same issue. I resolved it by using the code at: https://bioconductor.org/packages/release/bioc/vignettes/scone/inst/doc/sconeTutorial.R
oppose to the code at:
https://bioconductor.org/packages/release/bioc/vignettes/scone/inst/doc/sconeTutorial.html
The main difference I see is that the imputation is largely commented out in the Tutorial.R version (works) and is still present in the Tutorial.html (broken).
-----More specifically------
fnr_out = estimate_ziber(x = expr, bulk_model = TRUE,
pos_controls = rownames(expr) %in% hk,
maxiter = 10000)
imputation=list(none=impute_null, # No imputation
expect=impute_expectation) # Replace zeroes
impute_args = list(p_nodrop = fnr_out$p_nodrop, mu = exp(fnr_out$Alpha[1,]))
my_scone <- scone(my_scone,
imputation = imputation, impute_args = impute_args,
scaling=scaling,
k_qc=3, k_ruv = 3,
adjust_bio="no",
run=FALSE)
-----Should be replaced with------
my_scone <- scone(my_scone,
scaling=scaling,
k_qc=3, k_ruv = 3,
adjust_bio="no",
run=FALSE)
head(get_params(my_scone))