Simon, I had a typo in my code and should have used Stop for the column name rather than End. Try mymat <- <<the matrix="" you="" have="" below="">> uniqueChr <- unique(mymat[,"Chr"]) extractedDNA <- character(nrow(mymat)) for (chr in uniqueChr) { selected <- which(mymat[,"Chr"] == chr) extractedDNA[selected] <- as.character(Views(Mmusculus[[chr]], mymat[selected,"Start"], mymat[selected,"Stop"])) } Patrick Biddie, Simon (NIH/NCI) [F] wrote: > Hi Patrick, > > Thanks for your response. I will look into IRanges and Xstring. > I also tried your code, however it gives me the following error: > > >> mymat >> > Chr Start Stop > 1 chr9 79466420 79466570 > 2 chr6 50495860 50496010 > 3 chr8 19687900 19688050 > 4 chrX 90313740 90313890 > 5 chr4 117732780 117732930 > 6 chr11 4090400 4090550 > > >> uniqueChr <- unique(mymat[,"Chr"]) >> extractedDNA <- character(nrow(mymat)) >> for (chr in uniqueChr) { >> > + selected <- which(mymat[,"Chr"] == chr) > + extractedDNA[selected] <- as.character(Views(Mmusculus[[chr]], > + mymat[selected,"Start"], mymat[selected,"End"])) > + } > > Error in newViews(subject, start = start, end = end, names = names, Class = "XStringViews") : > 'start' and 'end' must be numeric vectors > In addition: Warning message: > In Views(Mmusculus[[chr]], mymat[selected, "Start"], mymat[selected, : > masks were dropped > > > Simon > > -----Original Message----- > From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] > Sent: Tuesday, September 01, 2009 2:21 PM > To: Biddie, Simon (NIH/NCI) [F] > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] obtain DNA sequence > > Simon, > Below is code that meets the needs of your explicit question > > mymat <- <<the matrix="" you="" have="" below="">> > uniqueChr <- unique(mymat[,"Chr"]) > extractedDNA <- character(nrow(mymat)) > for (chr in uniqueChr) { > selected <- which(mymat[,"Chr"] == chr) > extractedDNA[selected] <- as.character(Views(Mmusculus[[chr]], > mymat[selected,"Start"], mymat[selected,"End"])) > } > > The question I have for you is have you tried using the IRanges > framework to represent your ranges? It would make this type of > processing easier to perform. There is also write functions such as > write.XStringSet and write.XStringViews that provide export > functionality without requiring you to coerce the DNA sequences into > character vectors. > > > > Patrick > > > > Biddie, Simon (NIH/NCI) [F] wrote: > >> Dear All, >> >> I am trying to obtain DNA sequences (mouse) from chromosome coordinates. I am relatively new with R and Bioconductor and would appreciate any help. >> >> I have the following style matrix: >> >> Chr Start Stop >> 1 chr9 79466420 79466570 >> 2 chr6 50495860 50496010 >> 3 chr8 19687900 19688050 >> 4 chrX 90313740 90313890 >> 5 chr4 117732780 117732930 >> 6 chr11 4090400 4090550 >> >> I can use the following code to obtain a single sequence by typing in the chromosome number, start and stop manually: >> >> >> >>> library(BSgenome.Mmusculus.UCSC.mm9) >>> >>> >> >> >>> seq1 = subseq(Mmusculus$chr9,79466420,79466570) >>> >>> >> >> >>> as(seq1, "character") >>> >>> >> How would I do this for all the rows in a matrix to be output as a single txt or csv file? ... without having to type each row (I have up to 15,000!) one at a time. Please find below the sessionInfo. >> >> Thank you for any help, >> >> Simon >> >> >> >>> sessionInfo() >>> >>> >> R version 2.8.1 (2008-12-22) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.11 BSgenome_1.10.5 >> [3] Biostrings_2.10.22 IRanges_1.0.16 >> [5] R.utils_1.1.3 R.oo_1.4.6 >> [7] R.methodsS3_1.0.3 >> >> loaded via a namespace (and not attached): >> [1] grid_2.8.1 lattice_0.17-25 Matrix_0.999375-23 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >