Probelm in deconvolution

[biostat0903]

Dear author,
Our group hopes to use the Spatalk package. When we analyze the 10x Visium data, the function dec_celltype can not work.
Our code:

obj <- dec_celltype(obj,
                               sc_data = as.matrix(sc_count),
                               sc_celltype = celltype,
                               if_doParallel = T,
                               use_n_cores = N_CORES,
                              dec_result = decon_prop)

Error:

Error in { :
  task 14 failed - "error in evaluating the argument 'x' in selecting a method for function 'rowSums':
invalid character indexing"

Could you tell me the reason for the error? Thank you!

Best,
Sheng

[multitalk]

You can check length(intersect(rownames(st_data), rownames(sc_data))). See #26

[biostat0903]

Thanks for your fast reply.

intersect(rownames(st_data),rownames(sc_data)) %>% length
[1] 9510
 dim(st_data)
[1] 9817 7481
dim(sc_data)
[1] 26733 19311

Now, I try to use the intersection between sc_data and st_data to subset the two dataset.

Best,
Sheng

[biostat0903]

When I use the intersection to fit the model.
I also meet the error:

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'rowSums': invalid character indexing

[multitalk]

Can you show the colnames(obj@data$rawdata)[1:10], unique(celltype) and decon_prop[1:10, ]?
all(rownames(decon_prop) == colnames(obj@data$rawdata))? Is it TRUE?

[biostat0903]

Thanks for your fast reply.
I sent all my data to your email. When you have time, please help me to check that.
Best,
Sheng

[multitalk]

The reason is that the inconsistent names of decon_prop. I have fixed the bug. Thanks for your feedback.

[multitalk]

@biostat0903 The reason of error invalid character indexing when doing Parallel in dec_celltype() is the generation of NA data.frame in generated newmeta, which will not occur when if_doParallel = FALSE. I have finished dec_celltype(if_doParallel = FALSE) for your data without error. I have fixed this bug and you can have a try with if_doParallel = TRUE. Thanks a lot!

[multitalk]