Hi Chen, The encoded [a-z] values are a compressed representation of scores for graphical display. If you need the actual scores, there are download files here:
ftp://ftp.hapmap.org/hapmap/ld_data/2009-04_rel27/ The 00README.txt file in that directory describes the file format. Hope that helps, and if you have more questions, please let us know at [email protected] . Angie ----- Original Message ----- > From: "Chen Xie" <[email protected]> > To: "Greg Roe" <[email protected]> > Cc: [email protected] > Sent: Tuesday, March 27, 2012 6:47:19 PM > Subject: Re: [Genome] A question about encoded symbols on hg18 HapMap LD > Phased track > Hi Greg, > > Thanks for your reply! > > I am sure about having read all the information. Maybe I did not mention > my question clearly. My problem is that I do not understand the encoded > values [a-z] appears in those tracks. What values do these symbols > ([a-z]) stand for? How can I get the values from them? > > Best wishes, > Chen Xie > > > > > δΊ 2012/3/27 5:19, Greg Roe ει: > > Hi Chen, > > > > When viewing the schema make sure to read both the information in > > the > > 'description' column of the schema as well as the track description > > (scroll down the page). I believe these define what all the fields > > in > > question are. > > > > You may find additional information on the Haploview web site: > > http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/user-manual > > > > If something is still unclear, just let us know: [email protected] > > > > - > > Greg Roe > > UCSC Genome Bioinformatics Group > > > > On 3/23/12 10:46 PM, Chen Xie wrote: > >> Hi, > >> > >> I need to use information on hg18 HapMap LD Phased track. When I > >> read > >> the schema, I did not understand the meaning of encoded symbols in > >> dprime, rsquared, lod, avgDprime, avgRsquared, avgLod and tInt > >> fields. I > >> search for it on all UCSC help and faq documents, and also on > >> Google. > >> But I did not find any explainations. > >> > >> Could you tell me what is the meaning of encoded symbols, and how > >> can I > >> get the values from them please? And is there a detailed > >> instrcution > >> about it? > >> > >> Thanks very much! > >> > >> Best wishes, > >> Chen Xie > >> _______________________________________________ > >> Genome maillist - [email protected] > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
