Finally I found something that provides lower level examples. I was looking around the genetics package. I came across write.pop.file(genetics) and there I found the format of 'pedigree' files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html
That reference lays out exactly the format that is being used. "Farrel Buchinsky" <[EMAIL PROTECTED]> wrote in message news:[EMAIL PROTECTED] > >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. > ______________________________________________ R-help@r-project.org 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.
