error for running 'imbalance_score' function

[dahun73]

Hello :)

I'm new user for condiments package. I'm trying to follow tutorial using my data now. To compare imbalance score between different conditions, I tried using 'imbalance_score' function. However, error came out and I can not which one is wrong.

scores <- imbalance_score(rd = reducedDims(sce)$UMAP,
                          cl = colData(sce)$stim,
                          k=10, smooth = 10)

I annotated two conditions for name as 'stim'.

Following error is:

scores <- condiments::imbalance_score(rd = reducedDims(sce)$UMAP,
+                           cl = colData(sce)$stim,
+                           k=10, smooth = 10)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'imbalance_score' for signature '"missing"'

Is there any suggestion about this..?

Thanks

Dahun

[yudibedi]

What was the solution to this? I'm running in to the same issue

[HectorRDB]

HI, could you share the traceback() of that error?

[yudibedi]

HI, could you share the traceback() of that error?

3: stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA) 2: (function (classes, fdef, mtable) { methods <- .findInheritedMethods(classes, fdef, mtable) if (length(methods) == 1L) return(methods[[1L]]) else if (length(methods) == 0L) { cnames <- paste0("\"", vapply(classes, as.character, ""), "\"", collapse = ", ") stop(gettextf("unable to find an inherited method for function %s for signature %s", sQuote(fdef@generic), sQuote(cnames)), domain = NA) } else stop("Internal error in finding inherited methods; didn't return a unique method", domain = NA) })(list(structure("missing", package = "methods")), new("nonstandardGenericFunction", .Data = function (Object, ...) { standardGeneric("imbalance_score") }, generic = structure("imbalance_score", package = "condiments"), package = "condiments", group = list(), valueClass = character(0), signature = "Object", default = NULL, skeleton = (function (Object, ... 1: imbalance_score(rd = reducedDims(sce_all)$UMAP, cl = colData(sce_all)$age_inj, k = 20, smooth = 40)

[HectorRDB]

Can you tell me the output of

is(reducedDims(sce)$UMAP)
is(colData(sce)$stim)

[yudibedi]

is(reducedDims(sce_all)$UMAP) [1] "matrix" "array"
[3] "mMatrix" "AnyMatrix"
[5] "input" "mpinput"
[7] "listI" "output"
[9] "structure" "matrix_OR_array_OR_table_OR_numeric" [11] "vector" "vector_OR_factor"
[13] "vector_OR_Vector"

is(colData(sce_all)$stim) [1] "NULL" "OptionalFunction" "optionalMethod" "OptionalList"
[5] "OptionalCharacter" "character_OR_NULL" "DataFrame_OR_NULL" "Constraint_OR_NULL" [9] "data.frameOrNULL" "integer_OR_NULL" "Assays_OR_NULL" "output"

Thanks for the help :)

[HectorRDB]

As you can see, colData(sce_all)$stim is null. You are not providing a condition vector. Hope this helps.