[BioC] IRanges: interaction with model fitting

[Martin Morgan]

On 08/20/2010 02:38 PM, Kasper Daniel Hansen wrote:
> locfit is a package from CRAN for doing local regression (think
> loess).  It does not have a NAMESPACE, and it uses what to my casual
> eyes look like a pretty standard model setup.  But there is a strange
> thing happening when IRanges is loaded.  An example is best:
> 
> First get some data and define two functions that essentially does the same:
> 
> library(locfit)
> utils::data(anorexia, package = "MASS")
> myData <- anorexia
> tmp <- function(dat) {
>     anorex.1 <- glm(Postwt ~ lp(Prewt),
>                            family = "gaussian", data = dat)
> }
> tmp1 <- function(dat1) {
>     tmp2 <- function(dat2) {
>         anorex.1 <- locfit(Postwt ~ lp(Prewt),
>                            family = gaussian, data = dat2)
> 
>     }
>     tmp2(dat2 = dat1)
> }
> 
> tmp(myData)
> tmp1(myData)
> 
> This works great.  Now load IRanges and do the same
> 
> library(IRanges)
>> tmp(myData)
> Error in terms.formula(formula, data = data) :
>   'data' argument is of the wrong type
> 
> Enter a frame number, or 0 to exit
> 
> 1: tmp(myData)
> 2: locfit(Postwt ~ lp(Prewt), family = "gaussian", data = dat)
> 3: eval(m, sys.frame(sys.parent()))
> 4: eval(m, sys.frame(sys.parent()))
> 5: eval(expr, envir, enclos)
> 6: model.frame(formula = Postwt ~ lp(Prewt), data = dat)
> 7: model.frame.default(formula = Postwt ~ lp(Prewt), data = dat)
> 8: terms(formula, data = data)
> 9: terms.formula(formula, data = data)
> 
> Selection: 0
>> tmp1(myData)
> Error in inherits(x, "data.frame") : object 'dat2' not found
> 
> Enter a frame number, or 0 to exit
> 
>  1: tmp1(myData)
>  2: tmp2(dat2 = dat1)
>  3: locfit(Postwt ~ lp(Prewt), family = gaussian, data = dat2)
>  4: eval(m, sys.frame(sys.parent()))
>  5: eval(m, sys.frame(sys.parent()))
>  6: eval(expr, envir, enclos)
>  7: model.frame(formula = Postwt ~ lp(Prewt), data = dat2)
>  8: model.frame.default(formula = Postwt ~ lp(Prewt), data = dat2)
>  9: is.data.frame(data)
> 10: inherits(x, "data.frame")
> 
> Selection: 0
> 
> Clearly something seems wrong.  The error messages for tmp and tmp1
> are different.  Perhaps the lacking NAMESPACE for locfit makes a
> difference.  And locfit sets up the design matrix using a slightly
> different set of commands, that to my eye mostly look like an older
> paradigm.
> 
> Any idea on what happens and why this is affected by IRanges?

It traces to IRanges' promotion of eval to a generic. A workaround is

library(IRanges)
eval = base::eval

Creating the generic changes the value of 'envir' (the lazy evaluation
of sys.frame(sys.parent())) in the call, as shown with

> trace(eval, signature=c("ANY", "ANY"), tracer=quote(print(ls(envir))))
> tmp1(anorexia) ## 'locfit' envir
Tracing eval(m, sys.frame(sys.parent())) on entry
 [1] "base"    "cens"    "data"    "formula" "geth"    "i"       "lfproc"
 [8] "m"       "subset"  "Terms"   "weights" "z"
Error in inherits(x, "data.frame") : object 'dat2' not found

verus

> eval = base::eval
> trace(eval, tracer=quote(print(ls(envir))))
[1] "eval"
> tmp1(anorexia) ## 'tmp2' envir
Tracing eval(m, sys.frame(sys.parent())) on entry
[1] "dat2"

I don't think there is a robust way around this, but maybe others have a
good idea?

Martin
> 
> Kasper
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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