[Rcpp-devel] add new components to list without specifying list size initially

[Walrus Foolhill]

Ok, thanks for your answer, but I wasn't clear enough. So here are more
details of what I want to do.

I have one list named "probes":
probes <- list(chr1=data.frame(name=c("p1","p2"),
                 start=c(81,95),
                 end=c(85,100),
                 stringsAsFactors=FALSE))

I also have one list named "genes":
genes <- list(chr1=data.frame(name=c("g1","g2"), start=c(11,111),
end=c(90,190)),
                chr2=data.frame(name="g3", start=11, end=90))

I need to compare those two lists in order to obtain the following list
which contains, for each gene, the name of the probes included in it:
links <- list(chr1=list(g1=c("p1")))

Here is my R function (assuming that the probes are sorted based on their
start and end coordinates):

fun.l <- function(genes, probes){
  links <- lapply(names(genes), function(chr.name){
    if(! chr.name %in% names(probes))
      return(NULL)

    res <- list()

    genes.c <- genes[[chr.name]]
    probes.c <- probes[[chr.name]]

    for(gene.name in genes.c$name){
      gene <- genes.c[genes.c$name == gene.name,]
      res[[gene.name]] <- vector()
      for(probe.name in probes.c$name){
        probe <- probes.c[probes.c$name == probe.name,]
        if(probe$start >= gene$start && probe$end <= gene$end)
          res[[gene.name]] <- append(res[[gene.name]], probe.name)
        else if(probe$start > gene$end)
          break
      }
      if(length(res[[gene.name]]) == 0)
        res[[gene.name]] <- NULL
    }

    if(length(res) == 0)
      res <- NA
    return(res)
  })
  names(links) <- names(genes)
  links <- Filter(function(links.c){!is.null(links.c)}, links)
  return(links)
}

And here is the beginning of my attempt using Rcpp:

src <- '
using namespace Rcpp;

List genes = List(genes_in);
int genes_nb_chr = genes.length();
std::vector<std::string> genes_chr = genes.names();

List probes = List(probes_in);
int probes_nb_chr = probes.length();

std::vector< std::vector<std::string> > links;

// the main task is performed in this loop
for(int chrnum=0; chrnum<genes_nb_chr; ++chrnum){
  DataFrame genes_c = DataFrame(genes[chrnum]);
  // ... add code to map probes on genes, that is fill "links" ...
}

return wrap(links);
'

funC <- cxxfunction(signature(genes_in="list",
                                probes_in="list"),
                      body=src, plugin="Rcpp")

The problem starts quite early: when I compile this piece of code, I get
"error: call of overloaded ‘DataFrame(Rcpp::internal::generic_proxy<19>)’ is
ambiguous".

What should I do to go through the "probes" and "genes" lists given as
input? Maybe more generically, how can we go through a list of lists (of
lists...) with Rcpp?

2nd (small) question, I don't manage to use Rprintf when using inline, for
instance Rprintf("%d\n", i);, it complains about the quotes. What should I
do to print statement from within the for loop?

Thanks in advance. As my question is very long, I won't mind if you tell me
to find another way by myself. But maybe one of you can put me on the good
track.

On Thu, Aug 11, 2011 at 7:00 AM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> On 11 August 2011 at 03:06, Walrus Foolhill wrote:
> | Hello,
> | I need to create a list and then fill it sequentially by adding
> components in a
> | for loop. Here is an example that works:
> |
> | library(inline)
> | src <- '
> | Rcpp::List mylist(2);
> | for(int i=0; i<2; ++i)
> |   mylist[i] = i;
> | mylist.names() = CharacterVector::create("a","b");
> | return mylist;
> | '
> | fun <- cxxfunction(body=src, plugin="Rcpp")
> | print(fun())
> |
> | But what I really want is to create an empty list and then fill it, that
> is
> | without specifying its number of components before hand... This is
> because I
> | don't know in advance at which step of the for loop I will need to create
> a new
> | component. Here is an example, that obviously doesn't work, but that
> should
> | show what I am looking for:
> |
> | Rcpp::List mylist;
> | CharacterVector names = CharacterVector::create("a", "b");
>
> If you know how long names is, you know how long mylist going to be ....
>
> | for(int i=0; i<2; ++i){
> |   mylist.add(names[i], IntegerVector::create());
> |   mylist[names[i]].push_back(i);
>
> I don't understand what that is trying to do.
>
> | }
> | return mylist;
> |
> | Do you know how I could achieve this? Thanks.
>
> Rcpp::List is an alias for Rcpp::GenericVector, and derives from Vector.
> You
> can look at the public member functions -- there are things like
>
>    push_back()
>    push_front()
>    insert()
>
> etc that behave like STL functions __but are inefficient as we (almost
> always) need to copy the whole object__ so they are not recommended.
>
> When I had to deal with 'unknown quantities of data' returning I was mostly
> able to either turn it into a 'fixed or known columns, unknow rows' problem
> (easy, just grow row-wise) or I 'cached' in a C++ data structure first
> before
> returning to R via Rcpp structures -- and then I knew the dimensions for
> the
> to-be-created object too.
>
> Dirk
>
>
> --
> Two new Rcpp master classes for R and C++ integration scheduled for
> New York (Sep 24) and San Francisco (Oct 8), more details are at
>
> http://dirk.eddelbuettel.com/blog/2011/08/04#rcpp_classes_2011-09_and_2011-10
>
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