[GenABEL-dev] GenABEL: save.gwaa.data

[Stephan Kolassa]

Dear GenABEL developers (Yurii?),

I am trying to export quality-checked full genome data for analysis 
outside R (you may recall that I asked about modeling gene-environment 
interactions in GenABEL some months back). save.gwaa.data() seems to be 
exactly what I need. Unfortunately, I don't understand the human=FALSE 
encoding (I did my best, digging through the documentation and str() 
output), and human=TRUE exceeds my allocated memory, even after 
memory.limit(). You note on the save.gwaa.data help page that this could 
by addressed.

My dataset after QC contains 413 IDs and 838230 SNPs. Do you think you 
could tweak save.gwaa.data() so it could output human=TRUE data on a 
standard Win XP laptop?

If yes, how long would you think this would take you? (A couple of 
people are waiting for this, they would be very happy to have a rough 
idea about when we could move forward - and if they are too inpatient, I 
may need to find some other way to do this anyway.)

Otherwise, do you have any documentation that would explain the 
snp.data-class in a little more detail, so I could try making sense out 
of human=FALSE data myself? Or is there any specific GenABEL source code 
I should be looking at?

Sorry for imposing on you... and thank you once again for making GenABEL 
available!

Best regards
Stephan Kolassa