The haplo.score function has the parameter "miss.val", which is used to indicate what numeric values are used to indicate missingness. By default, miss.val=0. [I suspect this is a relic of a standalone form of the haplo.score program.] Under this coding, no row is completely observed, and they all get deleted, resulting in an empty data set. No variation indeed.
To resolve your problem, specify miss.val=NA. IE, > hscore<-haplo.score(y,geno,trait.type="binomial",miss=NA) -Greg > -----Original Message----- > From: X. Yu [mailto:[EMAIL PROTECTED] > Sent: Friday, March 07, 2003 2:27 PM > To: [EMAIL PROTECTED] > Subject: [R] help on haplo.score > > > Hi all, > > Recently i am running a new package call "haplo.score" in R > which compute > score statistics to evaluate the association of a trait with > haplotypes, when linkage phase is unknown. unfortunately, > I kept getting an error message like "No variation in y > values". where y > is my trait vector with 1 for disease and 0 for non-disease. > if someone > happen to know why i am getting this error, please let me > know. your help > is highly appreciated. > > see the following for a part of my data and code. > i have 5 loci and total 150 subjects, but here i only > includes 8 of them > > xuesong > > ## matrix for haplotype data (8x10) > geno<-matrix(c(0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0 > ,1, 0, 1, 0, 1, > 0, 0 ,0, 1, 0, 0, 0, 1, 0, 0,1, 1 ,0, 0, 1, 1, 0, 0, 1, > 1,),byrow=TRUE,ncol=10) > geno2<-matrix(c(0, 1, 0, 1, 0, 1, 0, 1, 0, 1,0, 1, 0, 1, 0, > 1, 0, 1, 0, > 1,1, 1, 0, 0, 1, 1, 0, 0, 0, 1,1, 1, 0, 0, 1, 1, 0, 0, 1, > 1),byrow=TRUE,ncol=10) > geno<-rbind(geno,geno2) > > ## trait data (binary) > y<-c(rep(0,4),rep(1,4)) > > ## compute score statistic > library(haplo.score) > hscore<-haplo.score(y,geno,trait.type="binomial") > > ______________________________________________ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > LEGAL NOTICE\ Unless expressly stated otherwise, this message is... [[dropped]] ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
