[BioC] no applicable method for "LD"

Basu, Analabha BasuA at humgen.ucsf.edu
Fri May 22 01:55:39 CEST 2009

Thanks Herve,
I did just that and it seems to work. Though i am no longer using a MS Windows Vista, but a linux.

Thanks again,

-----Original Message-----
From: Hervé Pagès [mailto:hpages at fhcrc.org]
Sent: Thu 5/21/2009 11:09 AM
To: Basu, Analabha
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] no applicable method for "LD"
Hi Basu,

Basu, Analabha wrote:
> Dear All at BioC,
> I have used the LD function a lot of times. However it does not seem to
> work in today's session.
> I am copying the outputs as well as the sessionInfo().

Your sessionInfo() indicates that you are not using the current release of
R + Bioconductor. Since we don't support old releases, I highly recommend
that you upgrade your installation (R-2.9.0 + BioC 2.4 is the current release).

There are 2 LD() functions: one defined in the genetics package, and the other
one defined in the GeneticsBase package. By default you get the former (because
genetics comes first in your search() path). If you want the latter, please use
fully qualified names e.g. GeneticsBase::LD()

Maybe in the past you didn't have this symbol masking issue because either
genetics was not on your way or it didn't have the LD() function...


> Any suggestions.
> --analabha
>> ld <- LD(MX_US)
> Error in UseMethod("LD", g1) : no applicable method for "LD"
>> sessionInfo()
> R version 2.8.1 (2008-12-22) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] fbat_1.6.0            GeneticsPed_1.4.0     genetics_1.3.4       
> [4] MASS_7.2-45           GeneticsDesign_1.10.0 gtools_2.5.0         
> [7] gmodels_2.14.1        gdata_2.4.2           GeneticsBase_1.8.0   
> [10] haplo.stats_1.3.8     mvtnorm_0.9-3         xtable_1.5-4         
> [13] combinat_0.0-6       
> loaded via a namespace (and not attached):
> [1] gplots_2.6.0 tools_2.8.1
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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