The human genome is arranged in 46 chromosomes. The longest is ~250 Mb (~2^28). While a Hilbert curve layout of a single chromosome tends to be informative, there is no obvious meaning in treating the complete human genome as a single 3 Gb linear sequence.
Wolfgang On 10/03/2017 21:54, Wolfgang Huber wrote:
Two replies: 1. Downsampling? In case you want to use the Hilbert curve for visualisation, please note that you will need a graphics device with resolution 65536 x 65536 to display it. Many people have smaller screens, so binning the genome (e.g. into bins of 10x10=100nt) could be a practical solution, and more efficient than computing some large intermediate thing that your graphics device will then downsample anyway. 2. Long vector In case you really need the big curve: I just had a look at the C code in the "HilbertVis" package, which anyway uses long ints, and it does not look difficult to modify the R wrapper so that it uses a long vector. I assume that Simon would welcome the patch. Wolfgang 9.3.17 08:44, Sohaib Ghani scripsit:I am trying to simulate hilbertcurve (of Bioconductor package) of level 16 in R. It takes about 4^16=4 Billion points. I want to generate the hilbert curve of genome (size about 3 billion). But I am getting this error long vectors not supported yet: memory.c:1668 I am using 64 bit version (R 3.3.2) so my guess is I can use vectors of length > 2^31. Also, my RAM is about 350GB. The command I am using is itr=4^16 hc = HilbertCurve(1, itr, 16, mode = "pixel", title = "pixel mode",start_from = "topleft") Even when I am reading the whole genome sometimes R is crashing in the process. I have read the other similar questions on this topic but could not find the solution. Please help me what should I use for this problem. Thanks [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Best wishes Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.hu...@embl.de http://www.huber.embl.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
