Dear all, I have been using package girafe to annotate my set of sequences. I have produced an object which is the overlap between my alignment file and the annotation information, but I am struggeling in how to export the table which contains per each row of the alignment information which type of RNA molecules it is. Can someone help? With kind regards, Andreia -- -------------------------------------------- Andreia J. Amaral, PhD Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]

Hi Andreia, please have a look at section 2.8 of the girafe vignette. The resulting object from interval_overlap(A,B) is a list of the same length as A with the i-th list element being the indices of B that overlap A[i]. Generating a character vector of overlapping RNA types can be done with 'sapply'. Assuming your annotation object is called 'B' and contains a vector 'type' specifying the type of RNA, and the overlap list is called 'Ov', the syntax would be something like this: ovTypes <- sapply( Ov, function(x) paste(B$type[x], collapse=",")) This vector 'ovTypes' is of the same length as the AlignedGenomeIntervals object, say 'A', and for exporting a table, you could use the function 'write.table': write.table(cbind(detail(A), type=ovTypes), ... < other arguments> ...) HTH, Joern On Mon, 28 Jun 2010 17:45:02 +0100, Andreia Fonseca wrote > Dear all, > > I have been using package girafe to annotate my set of sequences. I have produced an object which is the overlap between my alignment file and the annotation information, but I am struggeling > in how to export the table which contains per each row of the alignment information which type of RNA molecules it is. Can someone help? > With kind regards, > Andreia > -- > -------------------------------------------- > Andreia J. Amaral, PhD > Unidade de Imunologia Cl?nica > Instituto de Medicina Molecular > Universidade de Lisboa > email: andreiaamaral at fm.ul.pt > ? ? ? ? ?andreia.fonseca at gmail.com --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246927