The current R implementation of ICE may take a long time for a large number of probes with many SNPs. We are planning to shortly provide a faster version of ICE with C implmentation. In the meantime, please try to partition the SNP files into small pieces to run in parallel in a cluster if higher computational efficiency is needed.
Here is a minimal description of the usage of current R implementation.
- Download ICE.tar.gz or ICE.zip to your local computer and uncompress it. Make sure that there are ICE.R (source file), test_snps.tab (test snp files), test_exprs.tab (test expression files).
- Run R and type the following commands
> source('ICE/ICE.R')
> snps <- as.matrix(read.table('ICE/test_snps.tab'))
> exprs <- as.matrix(read.table('ICE/test_exprs.tab'))
> rst <- ICE.REMLt.batch(exprs,snps)
The last line may take up to 30 minutes. - For more sophisticated options with different context of eQTL mapping, please contact Hyun Min Kang