Hi Malcolm, Hermann, On 08/20/2013 06:05 AM, Cook, Malcolm wrote: >> Hello, > > > >I have some points according to the internal order of granges objects. > > > >1) Automatically there is an order depending on the a) seqnames (= > >chromosomes) and b) the ranges. > > no! There is no gaurantee on the order. > >> library(GenomicRanges) >> example(GRanges) > ... >> longGR > GRanges with 30 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <integer> > a chr1 [1, 10] - | 1 > b chr2 [2, 10] + | 2 > c chr2 [3, 10] + | 3 > d chr2 [4, 10] * | 4 > e chr1 [5, 10] * | 5 > ... ... ... ... ... ... > chr2 [106, 115] - | 26 > chr2 [107, 116] - | 27 > chr3 [108, 117] - | 28 > chr3 [109, 118] - | 29 > chr3 [110, 119] - | 30 > --- > seqlengths: > chr1 chr2 chr3 > 1000 2000 1500 >> rev(longGR) > GRanges with 30 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <integer> > chr3 [110, 119] - | 30 > chr3 [109, 118] - | 29 > chr3 [108, 117] - | 28 > chr2 [107, 116] - | 27 > chr2 [106, 115] - | 26 > ... ... ... ... ... ... > e chr1 [5, 10] * | 5 > d chr2 [4, 10] * | 4 > c chr2 [3, 10] + | 3 > b chr2 [2, 10] + | 2 > a chr1 [1, 10] - | 1 > --- > seqlengths: > chr1 chr2 chr3 > 1000 2000 1500 >> > > > > >2) The seqnames are always sorted in ascii order. > > No! but they _can_ be: > >> sort(longGR) > GRanges with 30 ranges and 1 metadata column: > seqnames ranges strand | score > <rle> <iranges> <rle> | <integer> > f chr1 [6, 10] + | 6 > chr1 [1, 5] - | 101 > a chr1 [1, 10] - | 1 > chr1 [2, 6] - | 102 > chr1 [3, 7] - | 103 > ... ... ... ... ... ... > j chr3 [ 10, 10] - | 10 > chr3 [ 10, 14] - | 110 > chr3 [108, 117] - | 28 > chr3 [109, 118] - | 29 > chr3 [110, 119] - | 30 > --- > seqlengths: > chr1 chr2 chr3 > 1000 2000 1500 Just a small point of clarification. The ordering of the seqnames in lexicographical order here is just a consequence of the fact that the seqlevels are already ordered in lexicographical order. If you change the order of the seqlevels first, then sort() will produce a different result: seqlevels(longGR) <- seqlevels(longGR)[c(2,3,1)] Then: > seqlevels(longGR) [1] "chr2" "chr3" "chr1" > sort(longGR) GRanges with 30 ranges and 1 metadata column: seqnames ranges strand | score <rle> <iranges> <rle> | <integer> b chr2 [2, 10] + | 2 c chr2 [3, 10] + | 3 chr2 [4, 8] - | 104 chr2 [5, 9] - | 105 chr2 [6, 10] - | 106 ... ... ... ... ... ... chr1 [ 3, 7] - | 103 chr1 [101, 110] - | 21 chr1 [102, 111] - | 22 chr1 [103, 112] - | 23 e chr1 [ 5, 10] * | 5 --- seqlengths: chr2 chr3 chr1 2000 1500 1000 Cheers, H. > > > ~ Malcolm Cook > > > > > >3) After > > df <- as.data.frame > > m <- regexpr ("\\d+", df$seqnames, perl=TRUE) > > df$Chromosome <- regmatches (df$seqnames, m) > > df$Chromosome <- as.integer (as.character (df$Chromosome)) > > df <- df [order(df$Chromosome),] > > only the order of the chromosomes is changed. The order of the ranges > >(now df$start and df$end) is still the same. > > > >Are my assumptions true? > > > >Thanks Hermann > > > > [[alternative HTML version deleted]] > > > >_______________________________________________ > >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 > > _______________________________________________ > 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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319