Displaying 3 results from an estimated 3 matches for "pgwide".
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2006 May 05
1
How to a handle an error in a loop
...step!
I am using dgc.genetics to run a TDT test on thousands of genetic loci. I
have learnt (through the help of others on this mailing list) to send the
complex output to useful data frames which in turn allow me to look at the
big picture and screen the thousands of loci.
Resultdt<-lapply(PGWide[,240:290], tdt)
the above would do 51 loci at a time. I want to do 6000 all in one shot.
the only problem is that about once every 100 variables in PGWide there is a
locus whose data trips up the tdt function. And when it does, it short
circuits the entire loop. Nothing gets written to Resultdt....
2006 May 07
0
How to a handle an error in a loop [Broadcast]
This ought to work:
resultdt <- lapply(PGWide[, 240:389], function(x, ...) try(tdt(x, ...)))
You can then check the class of each component to see which one failed.
Andy
From: Farrel Buchinsky
>
> "Berton Gunter" <gunter.berton at gene.com> wrote in message
> news:008601c67097$de1b46e0$5bc4fea9 at gne.windows.gen...
2006 May 02
4
Repeating tdt function on thousands of variables
...D the person 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 fu...