Hello, I have two mapped files from Chip_seq experiments produced by maq software. I read this files with the readAligned function from the ShortRead package. I just want to combine this two files in one, I am wondering if anyone know the best method to do this. I am trying to use rbind or cbind ? dataIP1<- readAligned(s_5_sequence.maq.map",type="MAQMap") dataIP2<- readAligned(s_6_sequence.maq.map",type="MAQMap") dataIP3<-... Thanks Arnaud.

Droit Arnaud wrote: > Hello, > > I have two mapped files from Chip_seq experiments produced by maq software. > I read this files with the readAligned function from the ShortRead package. > I just want to combine this two files in one, I am wondering if anyone know the best method to do this. I am trying to use rbind or cbind ? > > dataIP1<- readAligned(s_5_sequence.maq.map",type="MAQMap") > dataIP2<- readAligned(s_6_sequence.maq.map",type="MAQMap") > dataIP3<-... Hi Arnuad, append(dataIP1, dataIP2) unfortunately, only two at a time; see ?"AlignedRead-class" Martin > > Thanks > > Arnaud. > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

If you give several filenames you read them in jointly, like readAligned(pattern = "s_[56]_sequence.maq.map", type = "MAQMap") Kasper On Jan 8, 2010, at 11:29 AM, Droit Arnaud wrote: > Hello, > > I have two mapped files from Chip_seq experiments produced by maq software. > I read this files with the readAligned function from the ShortRead package. > I just want to combine this two files in one, I am wondering if anyone know the best method to do this. I am trying to use rbind or cbind ? > > dataIP1<- readAligned(s_5_sequence.maq.map",type="MAQMap") > dataIP2<- readAligned(s_6_sequence.maq.map",type="MAQMap") > dataIP3<-... > > Thanks > > Arnaud. > > _______________________________________________ > 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

Hi Arnaud, One option would always be to combine them with maq before reading them into R. Check out the 'mapmerge' command in maq. Cheers, Cei Droit Arnaud wrote: > Hello, > > I have two mapped files from Chip_seq experiments produced by maq software. > I read this files with the readAligned function from the ShortRead package. > I just want to combine this two files in one, I am wondering if anyone know the best method to do this. I am trying to use rbind or cbind ? > > dataIP1<- readAligned(s_5_sequence.maq.map",type="MAQMap") > dataIP2<- readAligned(s_6_sequence.maq.map",type="MAQMap") > dataIP3<-... > > Thanks > > Arnaud. > > _______________________________________________ > 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