R help - Feb 2008 - kinship package: drawing pedigree error

Hi

Im using the kinship package to draw a pedigree. On my data set this works fine
but when i add indivudals to the pedigree i keep getting an error i hope someone
can help me!

This is the code im using:

Data<-read.table("Tree.txt", header=T, 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
1,21142,9974,8858,2,0
1,23172,265,21142,2,0
1,25409,265,21142,1,0
1,23171,265,21142,2,0
1,265,NA,NA,1,0
1,9981,NA,NA,1,0
1,8853,NA,NA,2,0
1,9974,NA,NA,1,0
1,9980,NA,NA,1,0
1,9972,NA,NA,1,0
1,8856,NA,NA,2,0
1,9976,NA,NA,1,0
1,9971,NA,NA,1,0
1,9975,NA,NA,1,0
1,9970,NA,NA,1,0

1,9979,NA,NA,1,0
1,20644,9979,8862,2,0
1,20670,9979,8862,1,0

I tried putting nuclear families closer together in de pedigree but this
doesn't seem to help. All individuals have both parents in the pedigree or
have 2 missing parents.


I hope someone can help me with this!

Iris


     
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I tried replacing the missing parents with 0 but got the same error 

Error in if (min(pos2) < 0) { : missing value where TRUE/FALSE needed

Any other thoughts?

Iris 

Subject: Re: [R] kinship package: drawing pedigree error

On Wed, 06-Feb-2008 at 04:49AM -0800, Iris Kolder wrote:

[...]

|> 1,9979,NA,NA,1,0
|> 1,20644,9979,8862,2,0
|> 1,20670,9979,8862,1,0
|> 

|> I tried putting nuclear families closer together in de pedigree but
|> this doesn't seem to help. All individuals have both parents in the
|> pedigree or have 2 missing parents.

It's a while since I used that function, but IIRC, a missing parent is
set as 0, not NA.  

It might have changed since I used it, in which case ignore me.

HTH


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You can also draw pedigrees using the pedtodot() function from the gap
package.  It does however depend on graphviz (http://www.graphviz.org).

An article on drawing pedigrees in R is available in Bioinformatics
22(8):1013-1014 (see http://forums.gentoo.org/viewtopic-t-641204)

There _may_ also be some pedigree drawing functionality in the GeneticsPed
package thats part of the RGenetics project (see http://rgenetics.org/)
although at present there are a few unresolved problems with the package and
only the SVN version is available.

Neil


Iris Kolder wrote:
> 
> Hi
> 
> Im using the kinship package to draw a pedigree. On my data set this works
> fine but when i add indivudals to the pedigree i keep getting an error i
> hope someone can help me!
> 
> This is the code im using:
> 
> Data<-read.table("Tree.txt", header=T, sep=",")
> attach(Data)
> ped<-pedigree(id, dadid, momid, sex, aff)
> par(xpd=T)
> plot.pedigree(ped)
> 
> 
-- 
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