hello,
we want to do genomic blup in r.i know that use pedigree package.
the formule is
gblup( P~1,data=ped[,c('ID','P')],M=M,lambda=1/h2-1)
P:phenotype variance
ped:pedigree
M: matrix marker or genotype
my ped has 4500 ID.but my M has 9000 individual.becasue i have two row for each
ID in M matrix becasue each ID has two haplotype.how can i solve it.the formula
didnt solve.
sincerely
Sent from my iPhone
Hello, i made a population about 4500 individual.this has two sex(female and male).they had pedigree. i wanted to enter new indiviual but their ID of indiviual mustnot be same perivous and their ID number mustnot be bigger than 4500. first population's ID number is 1:4500. how can i handel it? Sent from my iPhone Begin forwarded message:> From: maryam firoozi <firoozi_maryam6858 at yahoo.com> > Date: January 18, 2016 at 1:14:56 AM GMT+3:30 > To: r-help at r-project.org > > hello, > we want to do genomic blup in r.i know that use pedigree package. > the formule is > gblup( P~1,data=ped[,c('ID','P')],M=M,lambda=1/h2-1) > P:phenotype variance > ped:pedigree > M: matrix marker or genotype > my ped has 4500 ID.but my M has 9000 individual.becasue i have two row for each ID in M matrix becasue each ID has two haplotype.how can i solve it.the formula didnt solve. > sincerely > > > Sent from my iPhone[[alternative HTML version deleted]]
Hi maryam, I think you have just restricted yourself to zero and negative numbers for the new cases. Well, I suppose there are imaginary numbers... Jim On Thu, Jan 21, 2016 at 8:26 AM, maryam firoozi via R-help < r-help at r-project.org> wrote:> Hello, > i made a population about 4500 individual.this has two sex(female and > male).they had pedigree. > i wanted to enter new indiviual but their ID of indiviual mustnot be same > perivous and their ID number mustnot be bigger than 4500. > first population's ID number is 1:4500. > how can i handel it? > > Sent from my iPhone > > Begin forwarded message: > > > From: maryam firoozi <firoozi_maryam6858 at yahoo.com> > > Date: January 18, 2016 at 1:14:56 AM GMT+3:30 > > To: r-help at r-project.org > > > > hello, > > we want to do genomic blup in r.i know that use pedigree package. > > the formule is > > gblup( P~1,data=ped[,c('ID','P')],M=M,lambda=1/h2-1) > > P:phenotype variance > > ped:pedigree > > M: matrix marker or genotype > > my ped has 4500 ID.but my M has 9000 individual.becasue i have two row > for each ID in M matrix becasue each ID has two haplotype.how can i solve > it.the formula didnt solve. > > sincerely > > > > > > Sent from my iPhone > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. >[[alternative HTML version deleted]]
Hello Maryam See below On 20/01/2016 21:26, maryam firoozi via R-help wrote:> Hello, > i made a population about 4500 individual.So you mean nearly 4500, not exactly 4500? this has two sex(female and male).they had pedigree.> i wanted to enter new indiviual but their ID of indiviual mustnot be same perivous and their ID number mustnot be bigger than 4500. > first population's ID number is 1:4500.If you tabulate ID you will get a table where all the entries should be 1 except for the ID which you have not yet used which will be zero. ?tabulate _NOT_ ?table All you need to do then is find them ?which should work> how can i handel it? > > Sent from my iPhone > > Begin forwarded message: > >> From: maryam firoozi <firoozi_maryam6858 at yahoo.com> >> Date: January 18, 2016 at 1:14:56 AM GMT+3:30 >> To: r-help at r-project.org >> >> hello, >> we want to do genomic blup in r.i know that use pedigree package. >> the formule is >> gblup( P~1,data=ped[,c('ID','P')],M=M,lambda=1/h2-1) >> P:phenotype variance >> ped:pedigree >> M: matrix marker or genotype >> my ped has 4500 ID.but my M has 9000 individual.becasue i have two row for each ID in M matrix becasue each ID has two haplotype.how can i solve it.the formula didnt solve. >> sincerely >> >> >> Sent from my iPhone > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. >-- Michael http://www.dewey.myzen.co.uk/home.html