R package, trying to lapply function to Biostring Views?

Question

First of all, I want to apologize if I am asking stupid questions, I have been only working for 2 days with R but I have to do it for my job.

I am trying to apply a function (calculate a product of matrices indexed by the name of a base pair) and I am using Biostrings to manage big sequences of DNA. I have to "window" these sequences into shorter sequences of 147 bp and apply a function to these shorter sequences.

So here's a MWE of what my code should look like (all this code is mine so it might be wrong, and I still do not understand the difference between = and <-):

MyMWEf <- function(seq, MAT){
  #MAT has colnames and rownames "BPs", for example "AG", "TA", etc.
  BPs = Views(seq, start = 1:(length(seq)-1), width = 2)
  BPs = unlist(lapply(BPs,toString)) 
  #With this I get a list of bps ("AG" "TA" etc.)
  AVGs = AVG[BPs, ]
  res=sum(AVGs)
}

MyMWE <- function(seq, MAT){
  seq <- Biostrings::DNAString(seq)
  windows <- Views(seq, start = 1:(length(seq)-146), width = 147)
  res = unlist(lapply(windows, MyMWEf, MAT))
}

Now, if I build a package with this and install it and run it, it gives me the following error:

 error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in as.list.default(X) : 
 No method to coerce this S4 class to a vector

So I started debugging, and found out that the problem comes in the lapply actually: It says error during wrapup. More specifically, it seems that the error comes when it tries to do as.list(windows). However, if I do the same but inside the console there is no error! I can lapply without problem for example lapply(windows,length) or even lapply(windows,MyMWEf,MAT) and everything works just fine (if I defined the function MyMWEf in the console), also if inside the console I write `as.list(windows)' it works.

If anybody could give me some insight in what am I doing wrong I would very much appreciate it!

Thank you

edited after narrowing down a bit (as.list problem).

Answer 1

The symptom you see is that the function works fine in an interactive session, but not within a package NAMESPACE.

This is usually because of an error in your package NAMESPACE file, and in particular you need to have in the DESCRIPTION part of your package the line

Imports: Biostrings

and in the NAMESPACE file something along the lines of

importMethodsFrom(Biostrings, as.list)

If you make heavy use of a package, then it might make more sense to have instead

import(Biostrings)

The Biocondcutor mailing list would be an appropriate place to post follow-up questions about using Biostrings.