问题
I tried to modify and redefine a function (xcmsRaw) in R package xcms by first defining a function
my.xcmsRaw <- function(filename, profstep = 1, profmethod = "bin",
profparam = list(mzcorrf=1), # PATCH - mzcorrf is the m/z correction factor, e.g. 0.99888 for long-chain hydrocarbons
includeMSn = FALSE, mslevel=NULL,
scanrange=NULL) { ... }
and then typing
unlockBinding("xcmsRaw", as.environment("package:xcms"))
assign("xcmsRaw", my.xcmsRaw, as.environment("package:xcms"))
lockBinding("xcmsRaw", as.environment("package:xcms"))
However, when I run it it gives me the error
Error in get(as.character(FUN), mode = "function", envir = envir) :
object 'profBinM' of mode 'function' was not found
caused by it not finding the profBinM function, which is a C code function defined in file xcms.c of the xcms package.
Any thoughts on how I could resolve this issue? (I am working under Windows 7, using R version 3.0.0)
回答1:
Thanks Josh - in my case I got it working now via
modifline='if ((profparam$mzcorrf!=1)&length(unique(rawdata$mz - trunc(rawdata$mz)))!=1) {rawdata$mz=rawdata$mz*profparam$mzcorrf} else if (profparam$mzcorrf!=1) {print("Exact masses were already rounded to nominal masses");profparam$mzcorrf=1}'
insertatline=6
trace(xcmsRaw, tracer=modifline,at=c(insertatline))
where I found the correct line to insert my modified code using
as.list(body(xcmsRaw))
To suppress the output of trace I then defined a second function
xcmsRaw2=function(...) {sink("NUL");obj=xcmsRaw(...);sink();return(obj) }
which can the be called and which does not provide any unnecessary tracing output.
Would still be nice to get it working via assignInNamespace() too though, as that would allow for more extensive edits/redefinitions and also for changes in the function arguments (which would be a common reason to redefine functions, that is, to take some extra argument)...
来源:https://stackoverflow.com/questions/16317706/redefining-a-function-in-an-r-package