[BioC] no method for coercing this S4 class to a vector
Martin Morgan
mtmorgan at fhcrc.org
Mon Mar 11 15:50:21 CET 2013
Hello Martin
Thanks a lot for your help. For me, if I try without as.character it
doesnt work.
But how you show, for you it works
I realize that you are using format="fastq" and I'm using
format="fasta"
I attached the file. But I dont want to use your time any more, you
already help me a lot.
I'm going to try to convert to fastq to see if I can get the same
result as you.
thank you very much
Thiago Maia
On 03/11/2013 07:06 AM, Thiago Maia wrote:
> function () {
> print(nchar(as.character(seq2[1])))
> }
>
> to execute
> fn1()
>
>
> actually the function became like this
> function (N) {
> for(i in as.numeric(1:N)) {
>
> print(substr(seq2[i],nchar(as.character(seq2[i]))-2,nchar(as.character(seq2[i]))))
> }
> }
Hi Thiago -- but the as.character() are not necessary
function (N) {
for(i in as.numeric(1:N)) {
print(substr(seq2[i], nchar(seq2[i])-2, nchar(seq2[i])))
}
}
and remember that R is 'vectorized', so
fn1 <- function(N) { ## better: function(N, seq2)
i <- 1:N ## better: i <- seq_len(N)
substr(seq2[i], nchar(seq2[i]) - 2, nchar(seq2[i]))
}
so after
library(Biostrings)
example(readDNAStringSet)
we have
> seq2 <- readDNAStringSet(filepath, format="fastq")
> fn1(10)
HWI-EAS88_1_1_1_1001_499 HWI-EAS88_1_1_1_898_392 HWI-EAS88_1_1_1_922_465
"TGT" "GAC"
"GGT"
HWI-EAS88_1_1_1_895_493 HWI-EAS88_1_1_1_953_493
HWI-EAS88_1_1_1_868_763
"AAA" "CTT"
"GCG"
HWI-EAS88_1_1_1_819_788 HWI-EAS88_1_1_1_801_123
HWI-EAS88_1_1_1_885_419
"CTT" "CTT"
"GTT"
HWI-EAS88_1_1_1_941_477
"AAT"
--
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