Herv?, Valerie, this function replaceAt() is doing exactly what i was looking for, thanks a lot!!!! robert. ps: FYI, the current version at SVN (.18) seems to break with the instruction below y <- .. but after checking out the very latest .19 the example works. On 09/16/2013 08:40 PM, Hervé Pagès wrote: > Hi guys, > > With Bioc-devel, you can use replaceAt() for this: > > x <- DNAStringSet(c("ATGACCACG", "ACTGGGGAA", "GCCGATGCG")) > y <- DNAStringSetList(DNAStringSet("G"), DNAStringSet("C"), > DNAStringSet("C")) > > Then: > > > replaceAt(x, IRanges(4, 4), y) > A DNAStringSet instance of length 3 > width seq > [1] 9 ATGGCCACG > [2] 9 ACTCGGGAA > [3] 9 GCCCATGCG > > An important clarification: An XString or XStringSet object is not more > immutable than a character vector or an R object in general in the > sense that we are not supposed to modify it *in-place*, except in some > particular situations where we know it's safe to do so. When it's not > safe to do so, then the object (or part of it) is copied and the copy > is modified. Of course all this is transparent to the end-user who > should never need to worry about whether it is safe or not to call [<-, > [[<- or replaceAt() on his/her DNAStringSet object: copies are made > if needed so those operations are always safe. > > Cheers, > H. > > > > On 09/16/2013 09:46 AM, Valerie Obenchain wrote: >> Hi, >> >> On 09/13/2013 07:13 AM, Robert Castelo wrote: >>> hi!! >>> >>> i'd like to know if there is some efficient way to replace a nucleotide >>> at a fixed position in a DNAStringSet object. >>> >>> let's say we have the following toy DNAStringSet object with 3 DNA >>> sequences: >>> >>> x <- DNAStringSet(c("ATGACCACG", "ACTGGGGAA", "GCCGATGCG")) >>> x >>> A DNAStringSet instance of length 3 >>> width seq >>> [1] 9 ATGACCACG >>> [2] 9 ACTGGGGAA >>> [3] 9 GCCGATGCG >>> >>> and a DNAStringSetList object with the following 3 nucleotides >>> >>> y <- DNAStringSetList(DNAStringSet("G"), DNAStringSet("C"), >>> DNAStringSet("C")) >>> y >>> DNAStringSetList of length 3 >>> [[1]] G >>> [[2]] C >>> [[3]] C >>> >>> i'd like to replace the, let's say, fourth nucleotide along the DNA >>> sequences in 'x' by those in 'y'. i can imagine how to do it coercing >>> back and forth to character and so on but i guess there must be some >>> more efficient way to do it. >> >> I don't think so. XString objects are immutable. The data are accessed >> through an external pointer to an environment where they are >> written/stored as raw. To subset/replace positions in 'x' with values >> from 'y' you would need to go through the 'as.character' conversion and >> create a new DNAStringSet. >> >> I've cc Herve in case I've gotten this wrong or he has a different >> solution to the problem. >> >> Valerie >> >> >> >> >> my interest come from the fact that the >>> DNAStringSet object i have to work with can have many DNA sequences. >>> >>> thanks!! >>> robert. >>> >> > -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550