[BioC] no method for coercing this S4 class to a vector

[Martin Morgan]

On 03/11/2013 06:43 AM, Thiago Maia wrote:
> Ops... sorry I just found (after many hours), it was so simple, how could take
> that long.. heheh
>
> nchar(as.character(seq2[i]))

I do not think you've identified your problem correctly; please provide a 
reproducible example -- what is 'l' ? For instance, after

   library(Biostrings)
   example(readDNAStringSet)

I can

 > seq2 = readDNAStringSet(filepath, format="fastq")
 > fn1 = function(N) nchar(seq2[l])
 > l = 2
 > fn1(l)
[1] 36

(but the function doesn't make much sense, usually the body of the function 
references arguments passed in to it). This is with

 > sessionInfo()
R version 2.15.2 Patched (2012-12-23 r61401)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BSgenome.Celegans.UCSC.ce2_1.3.19 BSgenome_1.26.1
[3] GenomicRanges_1.10.7              Biostrings_2.26.3
[5] IRanges_1.16.6                    BiocGenerics_0.4.0
[7] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] parallel_2.15.2 stats4_2.15.2   tools_2.15.2

Martin
>
> thanks
>
> Thiago Maia
>> Hello
>>
>>        - Sorry if this message appear twice, before I sent from the wrong
>> e-mail address(not registered)
>>
>>         I trying to make a function in R but I couldnt figure out whats
>> happening.
>>
>>         I loadded a fasta file.
>>         seq2 <- readDNAStringSet("c:/teste/testfile.txt","fasta")
>>
>>         I would like to get the length.
>>         If I execute directly all works
>>
>>         > nchar(seq2[1])
>>           Test_4489
>>                  90
>>
>>         But if I create a function
>>         function (N) {
>>            nchar(seq2[1])
>>         }
>>
>>         when I execute
>>         > fn1(1)
>>         Error in nchar(seq2[1]) :
>>         no method for coercing this S4 class to a vector
>>
>>         I tried things like as.vector(nchar(seq2[1])) but got the same
>> message.
>>
>>         Does anybody have a suggestion what I have to do or read.
>>
>> thanks a lot
>>
>> Thiago Maia
>>
>>
>> --
>>
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>
>
> --
>
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