Hi,
I would like to perform IBD analysis on exome dataset to identify disease-gene. The script I used is ibd2.R which invokes R module RHmm (Bioinformatics. 2011 Mar 15;27(6):829-36. 2011 Jan 28. Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders).The script requires an active internet connection to download recombination data from the UCSC database. Unfortunately, my workstation is unable to access to internet. So I follow the tutorial and have downloaded the recombination rate for hg19 from UCSC myself and the command line is like Rscript /path/to/idb2.R /path/to/test.ibs 2 /path/to/UCSC_recombineRate/hg19 >output.ibd. However, it seems that the script still try to connent UCSC. The error message is :
Loading required package: GenomeInfoDb
Error in function (type, msg, asError = TRUE) : couldn't connect to host
Calls: browserSession ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
I went through the IBD2-tutorial.pdf, but I still do not know how to fix this. The tutorial, ibd2.R and test.ibs I used are download from http://compbio.charite.de/contao/index.php/ibd2.html. Since I know little about R, would anyone giving me a clue on this?
Thank you!
Emma
