Solved: [R] piece wise application of functions
Itay Furman
itayf at fhcrc.org
Sat Feb 21 00:38:46 CET 2004
Thanks! Especially for pointing out the usage of a 'wrapper'
function in conjunction to lapply. In addition, data
re-organization was important, too, as you pointed out.
My final solution was slightly different than your proposition.
See below.
Thanks again,
Itay
On Fri, 20 Feb 2004, Tom Blackwell wrote:
> If it were my problem, I would re-structure the task around the
> existing capabilities of lapply(). In particular, I would
> concatenate the three lists of functions, then write a wrapper
> function which takes three arguments: an index, a list of
> functions and a data set. Then I would call lapply() twice
> to get the result you appear to be asking for. Here's a rough
> example, untested, which may not work exactly for your situation.
>
> miss.all <- c(missgp0, missgp1, missgp2)
> wrapper <- function(i, ff, d) {ff[[i]](d)}
> result.1 <- unlist(lapply(seq(9), wrapper, miss.all, snps.missgp[["ic"]]))
> result.2 <- unlist(lapply(seq(9), wrapper, miss.all, strs.missgp[["ic"]]))
> gaps <- c( # nine multiples of 1e+6 which describe the nine functions )
> result <- cbind(gaps=gaps, snps=result.1, strs=result.2)
>
# Make skeleton d.f. for the results
gaps <- data.frame(gap=paste(c(1, 2, 5), "+06", sep="e")
# Re-organize data :-)
# Each interpolation function will operate on a single row
markers <- ( markers <- cbind(strs.missgp[["ic"]],
snps.missgp[["ic"]]) )[1:3,]
# A slight different definition: makes explicit the application
# to rows
wrapper <- function(i, ff, d) {ff[[i]](d[i,])}
# Compute. Note the use of sapply()
case0 <- cbind(gaps, t(sapply(seq(3), wrapper, missgp0,
markers)))
case1 <- cbind(gaps, t(sapply(seq(3), wrapper, missgp1,
markers)))
case2 <- cbind(gaps, t(sapply(seq(3), wrapper, missgp2,
markers)))
gaps was a d.f.; therefore, cbind() coerces the result to d.f.
For example:
case0
gap strs snps
1 1e+06 46145.218 374.3882
2 2e+06 2547.841 494.0718
3 5e+06 1372.235 402.9667
> In this case, result is a matrix, not a data frame, but you can
> easily convert between the two.
>
> HTH - tom blackwell - u michigan medical school - ann arbor -
>
I tried to loop over the indices of case and missgp, 0,1,2,
using assign() but some how failed; and really wanted to go on
with the analysis.
Later, it occured to me that I might have used some wrapper
function in combination with outer(); and the result would be in
the diag()onal. That is because what in fact I was looking for
was an inner prodcut of a vector of functions, with a vector of
arguments.
Thanks again,
Itay
> On Thu, 19 Feb 2004, Itay Furman wrote:
>
> >
> > Dear all,
> >
> > After struggling for some time with *apply() and eva() without
> > success, I decided to ask for help.
> >
> > I have 3 lists labeled with, each contains 3 different
> > interpolation functions with identical names:
> >
> > > names(missgp0)
> > [1] "spl.1mb" "spl.2mb" "spl.5mb"
> > >
> > > names(missgp1)
> > [1] "spl.1mb" "spl.2mb" "spl.5mb"
> > >
> > > names(missgp2)
> > [1] "spl.1mb" "spl.2mb" "spl.5mb"
> > >
> >
> > (
> > In case it matters the functions accept and return one argument:
> > block.size <- spl.1mb(ic)
> > )
> >
> > Then, I have 2 data frames with identical structure:
> >
> > > snps.missgp
> > intvl.mb ic
> > 1 1e+06 0.597
> > 2 2e+06 0.504
> > 3 5e+06 0.327
> > 4 1e+07 0.204
> > >
> >
> > > strs.missgp
> > intvl.mb ic
> > 1 1e+06 0.67200
> > 2 2e+06 0.62325
> > 3 5e+06 0.51000
> > 4 1e+07 0.38775
> > >
> >
> > I would like to apply the functions on these data frames
> > piece-wise and create a data frame per function _list_.
> >
> > So I am looking for a final output like this:
> >
> > > case0
> > gap snps strs
> > 1 1e+06 .. ..
> > 2 2e+06 .. ..
> > 3 5e+06 .. ..
> >
> > Here, case0$snps[1] is, for example, the result of applying the
> > function in missgp0[1] on the entry snps.missgp$ic[1];
> > and, case0$strs[1] is the result of applying the same function
> > on strs.missgp$ic[1].
> >
> > Then, I want to repeat the whole thing with missgp1,2 instead
> > of missgp0, generating case1,2 data frames.
> >
> > How should I do it?
> >
> >
> > Thanks in advance,
> > Itay Furman
> >
> > --------------------------------------------------------------------
> > itayf at fhcrc.org Fred Hutchinson Cancer Research Center
> >
> > ______________________________________________
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> >
>
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