Sorry if this answer was already given, or if I miss the point,
but did you have a look to "lowerTriangle" and "upperTriangle" functions 
in the "gdata" package ?

# example
# A<-matrix(rnorm(9),3,3)
# B<-B<-matrix(NA,dim(A)[1],dim(A)[2])
# lowerTriangle(B)<-lowerTriangle(A)
# upperTriangle(B)<-lowerTriangle(A)
# diag(B)<-diag(A)

Hope this helps, sorry if it was already answered.
Olivier

-- 
Olivier ETERRADOSSI
Maître-Assistant
CMGD / Equipe "Propriétés Psycho-Sensorielles des Matériaux"
Ecole des Mines d'Alès
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http://www.ema.fr

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