Extract sequences from Class DNAbin

Question

[l.roca]

Hi,

In the script below, based on this, how can I extract the sequences from the Class DNAbin?

Thanks

require(ape) 

cotton_acc <- c("U56806", "U12712", "U56810",
                    "U12732", "U12725", "U56786", "U12715",
                    "AF057758", "U56790", "U12716", "U12729",
                    "U56798", "U12727", "U12713", "U12719",
                    "U56811", "U12728", "U12730", "U12731",
                    "U12722", "U56796", "U12714", "U56789",
                    "U56797", "U56801", "U56802", "U12718",
                    "U12710", "U56804", "U12734", "U56809",
                    "U56812", "AF057753", "U12711", "U12717",
                    "U12723", "U12726")

cotton <- read.GenBank(cotton_acc, species.names = T)

[mikhail.shugay]

Try lapply(cotton, as.character)

[ferroao]

this could help. cotton <- read.GenBank(cotton_acc, species.names = T, as.character=T)

Answer 1

[David W]

I'm not quite sure what you mean by "extract" here. The DNAbin object contains the sequences, which in this case behaves rather like a list:

typeof(cotton)

To extract elements from the object you can use either of the normal methods: $NAME, [[iINDEX]] or [INDEX]. If you are new to R you might want to check out? Extract to see how those methods differ.

EDIT

To answer the new question you could make your dataframe like this:

df <- data.frame(ID=labels(cotton),
                 sp=attr(cotton, "species"),
                 seq=sapply(cotton, paste, collapse=""))

[l.roca]

I do not know how to access the sequence as it is in the DNAbin object. the typeoff and the [] does not provide what I need.

[David W]

What do you need?

[l.roca]

Hi,

I wish to save the accession number, species name and the sequence in a data.frame.

Thanks

[David W]

Ok, answer edited.

[l.roca]

Thanks a lot