So a question that could have been asked in rcpp forum, but maybe you have already made a wrapper for it, so I ask here.

I want to access the ith row of a GRangesList:

#include <Rcpp.h>

using namespace Rcpp;

Environment envGRanges("package:GenomicRanges");

Function GRangesList = envGRanges["GRangesList"];


S4  getGRL_byIndex(S4  fiveUTR, int i ){
  S4 grangesObj("GRangesList");  
  grangesObj = as<GRangesList>fiveUTRs[i];

 return grangesObj;
}

Error is: no match for operator = (types: s4 and unresolved overload function type)

Is this possible to do ?

Very roughly, I would write my C++ code to rely on base R vectors as inputs, implement the body using standard C++ data structures, and return the output as a list of base R vectors

#include <Rcpp.h>

using namespace Rcpp;

// [[Rcpp::export]]
List orfs(
    CharacterVector seqname,
    IntegerVector start,
    IntegerVector end,
    IntegerVector input_index,
    CharacterVector fasta)
{
    std::vector<int> result_index;         // index of input that output belongs to
    std::vector<std::string> result_value; // output values
    // create result in C++
    // ...
    // then return to R, e.g., allowing many orf per input
    return List::create(
        Named("index") = wrap(result_index),
        Named("orf") = wrap(result_value));
}

and would write an R wrapper that works on the class at the R level

rorfs <- function(grl) {
    gr <- unlist(grl, use.names=FALSE)
    result <- orfs(
        as.character(seqnames(gr)),
        start(gr),
        end(gr),
        rep(seq_along(grl), lengths(grl)),
        "fasta"
    )
    ## manipulate result to final form
    orf <- NA_character_
    orf[result$index] <- result$orf
    gr$orf <- orf
    relist(gr, grl)
}