On Aug 5, 2010, at 3:59 PM, karena wrote:
library(GenABEL)
gs.b <- gs
> library(GenABEL)
Loading required package: MASS
GenABEL v. 1.6-0 (June 21, 2010) loaded
> gs.b <- gs
Error: object 'gs' not found
You are not making this easy. I asked what str(gs) returned. Instead
you gave us code but no data or even information about the data. There
was always a chance that gs was part of that package, so I installed
GenABEL and its 5 dependencies. The mind-reading abilities of most
listeRs, and especially mine, are fairly limited.
ok <- complete.cases(g...@phdata[,c('sex','age','b.dbp','b.bmi')])
gs.b <- gs.b[ok]
So what does str(gs.b) now look like?
g...@phdata <- g...@phdata[,c('id','sex','age','b.dbp','b.bmi')]
index=1:g...@gtdata@nsnps
ran.snp=sample(index,261,replace=F)
gs.b.gkin=ibs(gs.b[,ran.snp], weight="freq")
We might also need to see what str(gs.b.gkin) returned.
attach(g...@phdata)
age2 <- age^2
age3 <- age^3
I am not knowledgeable about GenABEL, but other regression programs
have functions for correctly generating polynomial terms.
##lm.bmi <- lm(bmi~age+age2+age3+sex)
##step.bmi <- step(lm.bmi)
##bmi.adj <- residuals(step.bmi)
h2.gs.b <- polygenic(b.dbp~age+age2+age3+sex+b.bmi, kin=gs.b.gkin,
data=gs.b)
I'm not sure if there was an assignment and creation of age2 and age3
inside gs.b. It might work, but there are weird gotcha's with attached
objects. I avoid it completely.
--
David.
######
Hi, david, above is my code. So I first removed the 3 individuals
who have
some missing data, then I performed the polygenic function with the
complete
data.
thanks,
karena
--
View this message in context:
http://r.789695.n4.nabble.com/an-issue-about-missing-data-tp2315094p2315536.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
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.
David Winsemius, MD
West Hartford, CT
______________________________________________
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.
