Hi all,

I'm having problems using the prunePed function in the MCMCglmm package and
wondered if anyone else had come across a similar issue. This is the code
that I run:

The unfixed pedigree file is called "pedigree" and the data containing the
phenotyped IDs is called "mydata". mydata contains a single record for each
of 5,161 individuals, but the full pedigree contains data on >82,000
individuals.

library(pedantics)
library(MCMCglmm)

fixedpedigree<-fixPedigree(Ped=pedigree)

keepIDs<-unique(mydata$ID)
length(keepIDs)

prunedpedigree<-prunePed(fixedpedigree, keep = keepIDs, make.base = FALSE)

The result is that I end up with a "prunedpedigree" file which contains
5,161 records- one for each phenotyped individual, giving their dam and
sire. However, it does not provide additional records for the parentage of
their parents or other informative relatives. I understand the difference
between make.base = TRUE and FALSE, and am sure that FALSE is correct.
However, using TRUE results in exactly the same outcome. Thus, is it likely
to be something related to how I've prepared the files? Or perhaps my use
of "keep = "? if anyone has any pointers, I'd be very grateful.

Best wishes,

Adam





-- 
Adam Hayward
Post-Doctoral Research Associate
Department of Animal and Plant Sciences
Alfred Denny Building
University of Sheffield
Western Bank
Sheffield S10 2TN
UK
http://www.huli.group.shef.ac.uk/adam-personal.html
http://adhayward.wordpress.com/
https://twitter.com/adhayward18

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