Hi, I would like to extract a txt file of a RangedData table I have created with TEQC package using the get.targets function and a bed target file "file" as an input: > targets<-get.targets("file", chrcol=1,startcol=2,endcol=3, zerobased=F, sep="\t",skip=0) [1] "read 1243 target regions in total, which are collapsed to 598 non-overlapping target regions" > targets RangedData with 598 rows and 0 value columns across 18 spaces space ranges | <factor> <iranges> | 1 Chr1 [115247090, 115250671] | 2 Chr1 [115250775, 115250813] | 3 Chr1 [115251152, 115251275] | 4 Chr1 [115252190, 115252349] | 5 Chr1 [115256421, 115256599] | 6 Chr1 [115258671, 115258798] | 7 Chr1 [115259279, 115259515] | 8 Chr10 [ 89622870, 89624305] | 9 Chr10 [ 89626430, 89626806] | ... ... ... ... 590 ChrX [133607389, 133607495] | 591 ChrX [133609211, 133609394] | 592 ChrX [133620495, 133620560] | 593 ChrX [133620692, 133620696] | 594 ChrX [133624218, 133624235] | 595 ChrX [133627538, 133627620] | 596 ChrX [133632420, 133632466] | 597 ChrX [133632638, 133632714] | 598 ChrX [133634060, 133634698] | I would like to extract the collapsed chromosome start and end points from this to a txt file? Any suggestions would be welcome... output file should contain: Chr1 115247090, 115250671 Chr1 115250775, 115250813 Chr1 115251152, 115251275 ..... Many thanks, Nat -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Hello Nathalie, Try this write.table(as.data.frame(targets)[,c(1,2,3)],file="./output.bed", quote=FALSE, sep="\t", row.names=FALSE, col.names=FALSE) Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 On Thu, Apr 19, 2012 at 11:29 AM, nathalie <nac at="" sanger.ac.uk=""> wrote: > > Hi, > I would like to extract a txt file of a RangedData table I have created with > TEQC package using the get.targets function and a bed target file "file" as > an input: > >> targets<-get.targets("file", chrcol=1,startcol=2,endcol=3, zerobased=F, >> sep="\t",skip=0) > > [1] "read 1243 target regions in total, which are collapsed to 598 > non-overlapping target regions" > >> targets > RangedData with 598 rows and 0 value columns across 18 spaces > ? ? ? space ? ? ? ? ? ? ? ? ranges ? | > <factor> <iranges> ? | > 1 ? ? ? Chr1 [115247090, 115250671] ? | > 2 ? ? ? Chr1 [115250775, 115250813] ? | > 3 ? ? ? Chr1 [115251152, 115251275] ? | > 4 ? ? ? Chr1 [115252190, 115252349] ? | > 5 ? ? ? Chr1 [115256421, 115256599] ? | > 6 ? ? ? Chr1 [115258671, 115258798] ? | > 7 ? ? ? Chr1 [115259279, 115259515] ? | > 8 ? ? ?Chr10 [ 89622870, ?89624305] ? | > 9 ? ? ?Chr10 [ 89626430, ?89626806] ? | > ... ? ? ?... ? ? ? ? ? ? ? ? ? ?... ... > 590 ? ? ChrX [133607389, 133607495] ? | > 591 ? ? ChrX [133609211, 133609394] ? | > 592 ? ? ChrX [133620495, 133620560] ? | > 593 ? ? ChrX [133620692, 133620696] ? | > 594 ? ? ChrX [133624218, 133624235] ? | > 595 ? ? ChrX [133627538, 133627620] ? | > 596 ? ? ChrX [133632420, 133632466] ? | > 597 ? ? ChrX [133632638, 133632714] ? | > 598 ? ? ChrX [133634060, 133634698] ? | > > > I would like to extract the collapsed chromosome start and end points from > this to a txt file? Any suggestions would be welcome... > > output file should contain: > Chr1 115247090, 115250671 > Chr1 115250775, 115250813 > Chr1 115251152, 115251275 > ..... > > > Many thanks, > Nat > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered office is 215 Euston Road, > London, NW1 2BE. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

If you're going to output the data as a BED file, then you're probably better off with: rtracklayer::export(targets, "my.bed") That makes it an actual BED, e.g. it converts the intervals to zero- based half-open. Michael On Thu, Apr 19, 2012 at 8:29 AM, nathalie <nac@sanger.ac.uk> wrote: > > Hi, > I would like to extract a txt file of a RangedData table I have created > with TEQC package using the get.targets function and a bed target file > "file" as an input: > > > targets<-get.targets("file", chrcol=1,startcol=2,endcol=3, zerobased=F, > sep="\t",skip=0) > > [1] "read 1243 target regions in total, which are collapsed to 598 > non-overlapping target regions" > > > targets > RangedData with 598 rows and 0 value columns across 18 spaces > space ranges | > <factor> <iranges> | > 1 Chr1 [115247090, 115250671] | > 2 Chr1 [115250775, 115250813] | > 3 Chr1 [115251152, 115251275] | > 4 Chr1 [115252190, 115252349] | > 5 Chr1 [115256421, 115256599] | > 6 Chr1 [115258671, 115258798] | > 7 Chr1 [115259279, 115259515] | > 8 Chr10 [ 89622870, 89624305] | > 9 Chr10 [ 89626430, 89626806] | > ... ... ... ... > 590 ChrX [133607389, 133607495] | > 591 ChrX [133609211, 133609394] | > 592 ChrX [133620495, 133620560] | > 593 ChrX [133620692, 133620696] | > 594 ChrX [133624218, 133624235] | > 595 ChrX [133627538, 133627620] | > 596 ChrX [133632420, 133632466] | > 597 ChrX [133632638, 133632714] | > 598 ChrX [133634060, 133634698] | > > > I would like to extract the collapsed chromosome start and end points from > this to a txt file? Any suggestions would be welcome... > > output file should contain: > Chr1 115247090, 115250671 > Chr1 115250775, 115250813 > Chr1 115251152, 115251275 > ..... > > > Many thanks, > Nat > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a company > registered in England with number 2742969, whose registered office is 215 > Euston Road, London, NW1 2BE. > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]