search for: hapmap

...igned but may not be used .ld.withmany: local variable ?nsnps.for.each? assigned but may not be used misinherits: local variable ?nc.snps? assigned but may not be used misinherits: local variable ?nr.snps? assigned but may not be used qq.chisq: local variable ?lab? assigned but may not be used read.HapMap.data: local variable ?base? assigned but may not be used read.HapMap.data: local variable ?build? assigned but may not be used read.HapMap.data: local variable ?finish? assigned but may not be used read.HapMap.data: local variable ?strand? assigned but may not be used tdt.snp: local variable ?nc.sn...

Dear R-list, Does somebody know how can I read a HUGE data set using R? It is a hapmap data set (txt format) which is around 4GB. After read it, I need to delete some specific rows and columns. I'm running R 2.6.2 patched over XP SP2 using a 2.4 GHz Core 2-Duo processor and 4GB RAM. Any suggestion would be appreciated. Thanks in advance, Jorge [[alternative HTML version delet...

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

...ignette. (Chinese/Tibetan/Arabic/Liangshan Yi was covered in a different vignette previously). More on this and emacs's multilingual extension further down. "snpMatrix Tutorial 2007" was the first ever tutorial written in spring 2007 [1]; it was pre-vignette and therefore had all the hapmap/pedfile output recorded verbatim; newly revived to work as a testsuite for input/output of hapmap/ped files (and flaged and fixed a few bugs introduced in the last few years). The bug fixes will appear in the upcoming snpMatrix 1.19.0.12, which hopefully will include some continual work to add read...

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and