[R] genetics package not working

[Farrel Buchinsky]

>From crawling around the internet it appears to me as if genetics has given 
way to GeneticsBase and is part of bioconductor. The basic data structure 
has changed to something called geneSet class. There is a pdf document that 
promises to help me. 
http://www.bioconductor.org/packages/2.1/bioc/vignettes/GeneticsBase/inst/doc/SummaryTables.pdf. 
Unfortunately it does not. My dataset which was created using genetics 
package does not seem to fit (or should I say "does not seem to easily fit") 
the read in formats demonstrated in the document: standard pedigree format, 
hapmap format, Pfizer format, Perlegen format.

Can anyone point me to a resource with lower level instructions and 
examples?

My format is as follows (rs numbers are not correct but do not worry about 
that detail)
> str(ped.seq[,2:15])
'data.frame':   608 obs. of  14 variables:
 $ pedigree  : int  1 1 2 3 3 4 4 5 6 6 ...
 $ id        : Factor w/ 30 levels "1","2","3","4",..: 3 2 3 3 2 3 2 3 3 2 
...
 $ id.father : int  1 0 1 1 0 1 0 1 1 0 ...
 $ id.mother : int  2 0 2 2 0 2 0 2 2 0 ...
 $ PtCode    : Factor w/ 608 levels "AJM16001FA","AJM16001MO",..: 74 73 77 
117 116 80 79 83 86 85 ...
 $ HS.nr     : int  32940 32941 32960 32963 32964 32967 32968 32970 32972 
32973 ...
 $ affected  : int  2 1 2 2 1 2 1 2 2 1 ...
 $ sex       : int  2 2 1 1 2 1 2 2 2 2 ...
 $ rs11684: Factor w/ 1 level "C/C": 1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "allele.names")= chr "C"
  ..- attr(*, "allele.map")= chr [1, 1:2] "C" "C"
 $ rs1144: Factor w/ 3 levels "A/A","G/A","G/G": 3 3 3 3 3 2 3 3 3 3 ...
  ..- attr(*, "allele.names")= chr  "G" "A"
  ..- attr(*, "allele.map")= chr [1:3, 1:2] "A" "G" "G" "A" ...
 $ rs120: Factor w/ 2 levels "A/A","A/G": 1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "allele.names")= chr  "A" "G"
  ..- attr(*, "allele.map")= chr [1:2, 1:2] "A" "A" "A" "G"



"Farrel Buchinsky" <fjbuch at gmail.com> wrote in message 
news:bd93cdad0706181709p563b55d4pe43e2d0ea894054d at mail.gmail.com...
> 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 : attempt to set an attribute on
> NULL
> In addition: Warning message:
> $ operator is deprecated for atomic vectors, returning NULL in:
> x$allele.names
>
> Clearly, I am missing something. What am I missing?
>
> -- 
> Farrel Buchinsky
>
> [[alternative HTML version deleted]]
>
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