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#$Author: sinnwell $
#$Date: 2006/10/13 16:44:43 $
#$Header: /people/biostat3/sinnwell/Projects/IBDReg/Make/RCS/setFounderAlleles.q,v 1.2 2006/10/13 16:44:43 sinnwell Exp $
#$Locker: $
#$Log: setFounderAlleles.q,v $
#Revision 1.2 2006/10/13 16:44:43 sinnwell
#ped$male did not exist, but ped$sex did.
#
#Revision 1.1 2006/10/10 21:21:47 sinnwell
#Initial revision
#
## authors: Dan Schaid and Dan Folie
## purpose: set founder alleles for a pedigree
## package: ibdreg
## date: Oct 2006
setFounderAlleles <- function(ped, x.linked=FALSE)
{
# changed chrom1 and chrom2 default missing values to 0 (rMarkFounders has NA)
#identify founders
founder <- ped$father == 0 & ped$mother == 0
male <- ped$sex==1
# n = number of alleles
n.male <- sum(founder & male)
n.female <- sum(founder & (!male) )
tmp1 <- tmp2 <- NULL
nSubj <- length(founder)
nMark <- 1
if(x.linked){
n.allele <- n.male + 2*n.female
a1.male <- 1:n.male
a2.male <- 1:n.male
a1.female <- seq((n.male+1), n.allele, by=2)
a2.female <- seq((n.male+2), n.allele, by=2)
} else {
n.allele <- 2*(n.male + n.female)
a1.male <- seq(1,2*n.male, by=2)
a2.male <- seq(2,2*n.male, by=2)
a1.female <- seq((2*n.male+1), n.allele, by=2)
a2.female <- seq((2*n.male+2), n.allele, by=2)
}
chrom1 <- chrom2 <- matrix(rep(0, nSubj * nMark), nrow = nSubj)
chrom1[founder & male, ] <- a1.male
chrom1[founder & (!male), ] <- a1.female
class(chrom1) <- "model.matrix"
chrom2[founder & male, ] <- a2.male
chrom2[founder & (!male), ] <- a2.female
class(chrom2) <- "model.matrix"
ped <- data.frame(ped, chrom1 = chrom1, chrom2 = chrom2)
return(ped)
}
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