Displaying 2 results from an estimated 2 matches for "phdata".
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2010 May 20
1
ERROR: cannot allocate vector of size?
...x86_64 Redhat cluster system. When I
log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am
randomly assigned to a x86_64 node.
I am using package GenABEL. My data (~ 650,000 SNPs, 3,000 people) loads in
okay and I am able to look at the data using basic commands [nids, nsnps,
names(phdata)]
The problem occurs when I try to run the extended analysis: xs <-
mlreg(GASurv(age,dm2)~sex,dta)
******************
1) I have looked through the memory limits on R
mem.limits()
nsize vsize
NA NA
2) Code:
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 961605 51...
2010 Nov 03
0
how to handle 'gwaa@gtdata' ?
I have a few questions about GenABEL, gwaa data.
1) is there a universal way that most GenABEL people use to add more
individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I
need to add some dummy parents, for 'gwaa at phdata', it's easy to add these
rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0
0.....' for all the dummy parents first. I am using the function
'convert.snp.ped', so I need a 'pedfile' of this format:
#ped id fa mo sex trait snp1.alle...