On Mon, Nov 7, 2011 at 6:00 PM, Minh Bui <buiduyminh at="" gmail.com=""> wrote: > HI Sean, > > Thank you for the quick answer. > > By correlation analysis, I mean I want to see if those HIV sequences fall > into the genes or not. If so, what kind of test I should do? Hi, Minh. Either source I sent should deal with that question easily. Overlaps of two sets of genomic regions are what both deal with very well. Sean > I will check those two sources out. > > Thanks, > > > > > On Mon, Nov 7, 2011 at 5:56 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> Hi, Minh. >> >> By "correlation analysis", you mean that you want to find the gene >> closest to each HIV site? ?If so, take a look at the GenomicRanges >> package. >> >> If you are more of a web server point-and-click person, take a look at >> using galaxy: >> >> http://main.g2.bx.psu.edu/ >> >> Sean >> >> >> On Mon, Nov 7, 2011 at 5:52 PM, Minh Bui <buiduyminh at="" gmail.com=""> wrote: >> > Hi everyone, >> > >> > I am new to Bioconductor and R. I did search through the list for my >> > problem but i can't find it. I am sorry if this question has been asked. >> > >> > I would like to perform a correlation analysis between a hiv data and >> gene >> > expression. >> > >> > Basically, i have a file that contains: hiv_name, start_position, >> > end_position, chromosome. I would like to see if these data has anything >> to >> > do with the location of our genes (I also have another file contains >> > gene_name, start_position, end_position, chromosome). >> > >> > What functions that allow me to do this? >> > >> > Hopefully someone can guide me to the right direction. >> > >> > >> > Thank you very much, >> > >> > -- >> > >> > >> ------------------------------------------------------------------- ----------------- >> > Minh Bui >> > Bioinformatic Research, MicroBiome Analysis Center >> > George Mason University, Prince William Campus >> > 10900 University Boulevard, MSN 4D4 >> > Manassas, Virginia ?20110 >> > http://mbac.gmu.edu >> > >> ------------------------------------------------------------------- ----------------- >> > >> > ? ? ? ?[[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 >> > >> > > > > -- > > -------------------------------------------------------------------- ---------------- > Minh Bui > Bioinformatic Research, MicroBiome Analysis Center > George Mason University, Prince William Campus > 10900 University Boulevard, MSN 4D4 > Manassas, Virginia ?20110 > http://mbac.gmu.edu > -------------------------------------------------------------------- ---------------- > > ? ? ? ?[[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 >