>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" <[EMAIL PROTECTED]> wrote in message news:[EMAIL PROTECTED] > 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]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
