It works. Indeed, I actually constructed the instance in sorted fashion but it got 're-ordered' by the function annotatePeakInBatch() from package ChIPpeakAnno. It's a very minor downside the package I believe.
Thank you, 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 Tue, Feb 9, 2010 at 6:30 PM, Michael Lawrence <[email protected]> wrote: > > > On Tue, Feb 9, 2010 at 3:21 PM, Ivan Gregoretti <[email protected]> wrote: >> >> Hi everybody, >> >> How do you sort a RangedData instance by start values? >> >> >> >> For instance, I have this example >> >> AannotatedRd[,0] >> >> RangedData with 10112 rows and 0 value columns across 25 spaces >> space ranges | >> <character> <IRanges> | >> 00029 chr1 [15794022, 15797422] | >> 00003 chr1 [ 5073247, 5076647] | >> 00004 chr1 [ 5503788, 5507188] | >> 00008 chr1 [ 6950752, 6954152] | >> 00010 chr1 [ 9072689, 9076089] | >> 00011 chr1 [ 9533772, 9537172] | >> 00019 chr1 [11535104, 11538504] | >> 00020 chr1 [11542979, 11546379] | >> 00021 chr1 [12113768, 12117168] | >> 00028 chr1 [14635606, 14639006] | >> ... >> <10102 more rows> >> >> (The next chromosome looks equally disordered) >> >> As you can see, the first row should not be at the top of the list. >> >> If this was a data.frame instance, I could solve it in no time with order(). >> >> How do you sort RangedData instances by start values (while keeping spaces >> separated)? >> > > rd[order(space(rd), start(rd)),] should work. Might be easier to construct it > sorted. > > Michael > >> >> Thank you, >> >> 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 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
