Jeff Newmiller jdnewmil at dcn.davis.CA.us
Thu Jun 20 23:48:56 CEST 2013

Re-posting, particularly without referencing your earlier post, is bad mailing-list etiquette. Posting in HTML is particularly frowned upon here also. Nor is this a statistical methods support forum... it is about R. I for one am finding your question very jargonish and obscure. If your question is straightforward in the genetics domain then there might be more responsiveness in the Bioconductor mailing list. Otherwise, you may need to frame your question more directly in terms of the R language, with an example starting data set and expected results [1].

You are also expected to read the Posting Guide mentioned at the end of every R-help email.

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
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Sent from my phone. Please excuse my brevity.

"Vallejo, Roger" <Roger.Vallejo at ARS.USDA.GOV> wrote:

>Dear R Users,
>I have always used ASReml, MTDFREML, SAS, etc. to estimate genetic
>correlation (Rg) between two continuous quantitative traits (also
>continuous and binary trait) but I have never used R package to
>estimate Rg. However, I use R package for many of my other statistical
>analysis needs. The R package is a great tool that has advanced to a
>level that now we can estimate whole genome-enabled breeding values in
>genomic selection research. So, with the aim of moving out of those
>packages (listed above) which are either expensive or have little
>support, I would like to know if we can estimate Rg between two binary
>traits (disease status: alive vs. dead) with the R package.
>My data: we have 100 full-sib (FS) families, and two random samples
>(each with n= 200 FS fish) from each FS family were evaluated for
>resistance response to two different bacterial diseases, separately. It
>implies that both traits are not recorded in the same individual; each
>trait is recorded in different groups of full-sibs (random sampled from
>a FS family). So using this family relationship (full-sibs), I would
>like to estimate the Rg between these two disease resistance traits; of
>course I would like to estimate Rg with the R package. I will
>appreciate having directions on which R package to use if any, or
>combination of R functions needed to use to calculate the Rg (between
>two binary traits; disease survival traits).
>Thank you very much in advance for your help.
>Roger L. Vallejo, Ph.D.
>U.S. Department of Agriculture, ARS, NCCCWA
>Voice:  (304) 724-8340 Ext. 2141
>Email:  roger.vallejo at ars.usda.gov<mailto:roger.vallejo at ars.usda.gov>
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>R-help at r-project.org mailing list
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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