Displaying 11 results from an estimated 11 matches for "famid".
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fami
2010 Aug 04
5
Question regarding significance of a covariate in a coxme survival model
Hi,
I am running a Cox Mixed Effects Hazard model using the library coxme. I
am trying to model time to onset (age_sym1) of thought problems (e.g.
hearing voices) (sym1). As I have siblings in my dataset, I have
decided to account for this by including a random effect for family
(famid). My covariate of interest is Mother's diagnosis where a 0 is
bipolar, 1 is control, and 2 is major depression. I am trying to fit
the following model.
thorp1 <- coxme(Surv(age_sym1, sym1) ~ lifedxm + (1 | famid), data =
bip.surv)
Which provides the following output:
-----------------...
2010 Jul 22
2
Multilevel survival model
* Please cc me if you reply as I am a digest subscriber *
Hi,
I am wondering how I can run a multilevel survival model in R? Below is
some of my data.
> head(bi0.test)
childid famid lifedxm sex age delta
1 22.02 22 CONTROL MALES 21.36893 0
2 13.02 13 MAJOR MALES 21.18001 0
3 64.02 64 CONTROL MALES 20.09377 0
4 5.02 5 CONTROL FEMALES 19.94524 0
5 183.02 183 BIPOLAR FEMALES 19.87406 0
6 37.02 37 BIPOLAR MALES 1...
2010 Jul 27
0
AIC from coxme
Hi,
I am running the following model:
fit1.full <- coxme(Surv(age_sym1, sym1) ~ sex + lifedxm*sex + (1|famid),
data=bip.surv)
I would like to extract the AIC from that object to calculate the AICC.
However, when I look at str(fit1.full) and summary(fit1.full) (pasted
below) I don't see anything that would allow me to get pull the AIC out
from that object.
Is there a way to retrieve the AIC from a c...
2010 Aug 31
1
any statement equals to 'goto'?
...---------------------------------------------------------------------
result <- matrix(NA, nrow=1, ncol=5)
for(i in 1:(nsnp-1)) {
for(j in (i+1):nsnp){
tempsnp1 <- data.lme[,i]
tempsnp2 <- data.lme[,j]
fm1 <- lme(trait~sex+age+rmtemp.b+fc+tempsnp1+tempsnp2+tempsnp1*tempsnp2,
random=~1|famid, na.action=na.omit)
fm2 <- lme(trait~sex+age+rmtemp.b+fc+tempsnp1+tempsnp2, random=~1|famid,
na.action=na.omit)
result[1,1] <- i
result[1,2] <- j
result[1,3] <- colnames(data.lme)[i]
result[1,4] <- colnames(data.lme)[j]
result[1,5] <- 2*(summary(fm1)$logLik-summary(fm2)$logLik)
if...
2006 Apr 27
2
Incomplete Trio in TDT analysis
...nt Proportion
1 73 0.7
2 31 0.3
NA 40 NA
Genotype Frequency:
Count Proportion
1/1 26 0.5
1/2 21 0.4
2/2 5 0.1
NA 20 NA
Heterozygosity (Hu) = 0.4225168
Poly. Inf. Content = 0.3309022
tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected )
Transmission/disequilibrium test
Data: Genotype.914186
Untransmitted allele frequencies, informative transmissions
and exact P-values
Allele Frequency Transmitted Untransmitted P-value
2 0.3333 3...
2006 May 02
4
Repeating tdt function on thousands of variables
...son ID etc. Thereafter
each variable is a specific locus or marker. The variables are named by a
pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which
is the name or id of the locus.
I am able to get the tdt to run by each locus. >tdt(Genotype.914186, PGWide,
famid, pid, fatid, motid, sex, affected )
Clearly I cannot type each locus in one at a time. Instead I want to loop it
but am not sure how to do it. I tried lapply but it did not really work.
The example in Dalgaard's book, >sapply( thuesen, mean, na. rm= T) seems to
work with basic functions...
2010 Sep 08
0
How to get OR and CI from GEE R package
Hi,
I am fitting a GEE model using gee R package, but I am not sure how to get
OR and its CI?
Could anyone give me some hints?
Here are some output:
> gee.obj <- gee(Affection~Sibsex+Probandsex,id = FAMID,family = binomial,corstr = "independence",data =seldata)
Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
running glm to get initial regression estimate
(Intercept) Sibsex2 Probandsex2
-1.6067213 0.3495830 0.5645009
> summary(gee.obj)
GEE: GENERALIZED LINEAR MOD...
2012 Oct 29
4
replace repeated id in a pedigree list
Hello,
I have a pedigree file such this:
FAMID ID FA ID MO ID SEX STATUS
1 1 0 0 2 0
1 2 3 1 2 2
1 4 3 1 1 2
1 5 3 1 1 0
1 6 3 1 1 0
1 7 3 1 2 2
1 8 3 1 1 0
1 9 3 1 1 0
1 10 3 1 2 0
1 11 3...
2012 Nov 09
0
Kinship2 and GenABEL
Hi,
I'm using kinship2 to calculate heritabilty, but I would like calculate in
GenABEL too.
I trying the code:
> require(kinship2)
> require(GenABEL)
> pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX,
famid=FID, missid=0))
> kmat = kinship(pedig)
> (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat))
Erro em intI(i, n = d[1], dn[[1]], give.dn = FALSE) :
invalid character indexing
>
How can I calculate heritabilty using GenABEL with kinship matrix of
kinship2 package?
Thanks,
-...
2008 Feb 06
2
kinship package: drawing pedigree error
...sep=",")
attach(Data)
ped<-pedigree(id, dadid, momid, sex, aff)
par(xpd=T)
plot.pedigree(ped)
This is my data looks like without the last 3 individuals it works perfect,when i add them i get the following error:
Error in if (min(pos2) < 0) { : missing value where TRUE/FALSE needed
famid,id,dadid,momid,sex,aff
1,8860,9972,8856,2,0
1,8855,9972,8856,2,0
1,8859,9976,8860,2,0
1,8854,9971,8855,2,0
1,8863,9975,8859,2,0
1,8858,9975,8859,2,0
1,8865,9975,8859,2,0
1,9969,9970,8854,1,0
1,8864,9980,8863,2,0
1,8862,9980,8863,2,0
1,23834,9981,8865,2,0
1,9968,9969,8853,1,0
1,21141,9974,8858,1,0
1...
2006 Apr 06
4
Reshaping genetic data from long to wide
Bottom Line Up Front: How does one reshape genetic data from long to wide?
I currently have a lot of data. About 180 individuals (some
probands/patients, some parents, rare siblings) and SNP data from 6000 loci
on each. The standard formats seem to be something along the lines of Famid,
pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2,
locus2Allele1, locus2Allele2, etc
In other words one human, one row. If there were multiple loci then the
variables would continue to be heaped up on the right. This kind of
orientation, shall be referred to as "wide".
Giv...