[adegenet-forum] dataset too large?
Thomas, Evert (Bioversity-Colombia)
E.Thomas at CGIAR.ORG
Fri Jul 1 20:55:45 CEST 2011
I am new to R so apologies for my ignorance, but I have a couple of
I am trying to use adegenet (on a 64bit system, windows7) for analyzing
a SSR dataset. It consists 96 loci and I have >25000 individuals (after
resampling). I have loaded the database as a dataframe in R, but am not
able to convert to genind format (PC physical memory becomes saturated,
while only 10% of CPU is used) . Could this be related to the size of my
dataset? Any suggestions?
On another note: Alternatively, I tried importing my data to genind
object from the corresponding file in Structure format. However, my
version of Structure (2.3.3.) does not seem to generate .stru or .str
files, any solution there?
And a last point: I am unable to install/load the R application
multicore because it is not among the packages list...
This is what I have done:
I did a read.csv with "header=T", and then rownames<-cacaoCSV[,1]
The problems occurs with the following command
cacao<-df2genind(cacaoCSV, sep="/",ind.names=NULL, loc.names=NULL,
pop=cacaoCSV[,2], missing=NA, ploidy=2, type="codom")
Many thanks in advance for any advice or suggestion you might have!
Enjoy the weekend
Evert Thomas, PhD
Associate Expert, Conservation and Use of
Forest Genetic Resources in Latin America
Regional Office for the Americas
Recta Cali-Palmira Km 17 - CIAT
P.O. Box 6713
Tel. 57 2 4450048 / 49 Ext 113
Fax 57 2 4450096
Email: e.thomas at cgiar.org <mailto:e.thomas at cgiar.org>
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