Beginner needs help with R
Hi Nabila,
This is because you ask to create a sequence with seq(), which does not
make much sense with non numeric data. That's why R trims the 0.
One alternative would be:
seq2 <- paste("DQ0", seq(60054, 60060), sep = "")
Would that work for you?
HTH,
Ivan
--
Ivan Calandra, PhD
MONREPOS Archaeological Research Centre and
Museum for Human Behavioural Evolution
Schloss Monrepos
56567 Neuwied, Germany
calandra at rgzm.de
+49 (0) 2631 9772-243
https://www.researchgate.net/profile/Ivan_Calandra
https://rgzm.academia.edu/IvanCalandra
https://publons.com/author/705639/
On 06/02/2017 02:50, Nabila Arbi wrote:
Dear R-Help Team!
I have some trouble with R. It's probably nothing big, but I can't find a
solution.
My problem is the following:
I am trying to download some sequences from ncbi using the ape package.
seq1 <- paste("DQ", seq(060054, 060060), sep = "")
sequences <- read.GenBank(seq1,
seq.names = seq1,
species.names = TRUE,
gene.names = FALSE,
as.character = TRUE)
write.dna(sequences, "mysequences.fas", format = "fasta")
My problem is, that R doesn't take the whole sequence number as "060054"
but it puts it as DQ60054 (missing the zero in the beginning, which is
essential).
Could please tell me, how I can get R to accepting the zero in the
beginning of the accession number?
Thank you very much in advance and all the best!
Nabila
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