Combine dispatch problems

[amcdavid]

doubleid <- data.frame(id1=1:3, id2=1:3, et=rep(3, 3), f1=rep('A', 3)) smallsc <- SingleCellAssay(doubleid, idvars='id1', geneid='f1', primerid='f1', measurement='et') spl <- split(smallsc, 'id1') c2 <- combine(spl[[1]], spl[[2]], spl[[3]]) #Works fine

c2 <- do.call(combine, spl@set)

cannot coerce type 'closure' to vector of type 'character' 1: do.call(combine, spl@set) 2: structure(function (x, y, ...) { if (length(list(...)) > 0L) { callGeneric(x, do.call(callGeneric, list(y, ...))) } else { standardGeneric("combine") } }, generic = structure("combine", package = "BiocGenerics"), package = "BiocGenerics", group = list(), valueClass = character(0), signature = c("x", "y"), default = \001NULL\001, skeleton = function (x, y, ...) stop("invalid call in method dispatch to \"combine\" (no default method)", domain = NA)(x, y, ...), class = structure("nonstandardGenericFunction", package = "methods"))(1 = <S4 object of class structure("SingleCellAssay", package = "SingleCellAssay")>, 2 = <S4 object of class structure("SingleCellAssay", package = "SingleCellAssay")>, 3 = <S4 object of class structure("SingleCellAssay", package = "SingleCellAssay")>) 3: callGeneric(x, do.call(callGeneric, list(y, ...))) 4: as.character(call[[1L]]) 5: as.character.default(call[[1L]])

[amcdavid]

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

[gfinak]

combine takes two argument, not more.. it's not suitable for enclosing within a do.call()

---

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 12:09 PM, Andrew McDavid wrote:

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

— Reply to this email directly or view it on GitHub.

[gfinak]

The solution would be to write a wrapper that recursively calls combine, while maintaining the caller's environment so as not to pollute the stack, I think.

---

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 12:09 PM, Andrew McDavid wrote:

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

— Reply to this email directly or view it on GitHub.

[gfinak]

This would be a suitable template (from reshape)

merge_recurse function (dfs, ...) { if (length(dfs) == 2) { merge(dfs[[1]], dfs[[2]], all = TRUE, sort = FALSE, ...) } else { merge(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort = FALSE, ...) } }

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 12:09 PM, Andrew McDavid wrote:

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

— Reply to this email directly or view it on GitHub.

[amcdavid]

It takes ... it appears? On Oct 4, 2012 12:39 PM, "Greg Finak" notifications@github.com wrote:

combine takes two argument, not more.. it's not suitable for enclosing within a do.call()

---

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 12:09 PM, Andrew McDavid wrote:

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/1#issuecomment-9154267.

[gfinak]

Well, you're right it should.. but it gives an error irrespective of the data type I'm passing to combine via do.call.

rbind and c and cbind all take (...) as the first argument.. may have something to do with it.

---

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 1:39 PM, Andrew McDavid wrote:

It takes ... it appears? On Oct 4, 2012 12:39 PM, "Greg Finak" notifications@github.com wrote:

combine takes two argument, not more.. it's not suitable for enclosing within a do.call()

---

Greg Finak, Ph.D Staff Scientist Vaccine and Infectious Disease Division. Fred Hutchinson Cancer Research Center Seattle, WA (206)667-3116 gfinak@fhcrc.org

On 2012-10-04, at 12:09 PM, Andrew McDavid wrote:

Or as long as we can somehow dispatch combine on a variable number of SingleCellAssays, it doesn't really matter if it works through do.call.

This looks pretty hairy, since it has to do with how combine is being dispatched by BiocGenerics, I think.

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/RGLab/SingleCellAssay/issues/1#issuecomment-9154267.

— Reply to this email directly or view it on GitHub.

[gfinak]

I've written a combine_recurse method to handle this.