search for: ldheatmap

Dear R-helpers, I am developing a package named LDehatmap. It depends on the "genetics" package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help >>> Building/Updating help pages for package 'LDheatmap' Formats: text html latex example LDheatmap text html latex example ldheatmap text html latex example Error: object 'reorder'...

Dear R wizards, I am seeking advice on graphics in R. Specifically, how to manipulate the size and save a plot I have produced using the LDheatmap library. I confess I am relatively new to graphics in R, but I would greatly appreciate any suggestions you may have. LDheatmap produces a coloured triangular matrix of pairwise associations between 600 genetic markers in my dataset. Initially the graphical output was confined to the com...

Version 0.2 of the package LDheatmap is now on CRAN. The main function LDheatmap produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot. The revisions to the package are aimed at i...

...nly need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents. Hope that help...

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

...s (4.0-3), gamlss.add (4.0-1), gamlss.data (4.0-1), genoPlotR (0.5.1), GEOmap (1.5-9), GEVcdn (1.0.2), GillespieSSA (0.5-4), gllm (0.33), glmperm (1.0-3), gRapHD (0.1.7), HFWutils (0.9.4.2010.08.20), hts (1.3), HWEintrinsic (1.1.1), igraph (0.5.4-1), intervals (0.13.3), ipw (1.0-6), laeken (0.1.3), LDheatmap (0.2-9), lme4 (0.999375-35), lmPerm (1.1-2), lordif (0.1-6), lpSolveAPI (5.5.2.0), magma (0.2.1-3), MCMCglmm (2.06), mondate (0.9.08.15), mondate (0.9.08.19.02), mratios (1.3.13), nacopula (0.4-3), nleqslv (1.7), nlt (2.1-1), NMF (0.5), pROC (1.3.1), qpcR (1.3-1), qpcR (1.3-0), qtl (1.18-7), qualit...

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