I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for related individuals in the analysis of a quantitative trait. GenABEL also has many other nice features for analysis and visualization of GWAS data that you can't find in PLINK, it's free, cross-platform, and implemented in R. I'll write another post about GenABEL later, but here I wanted to note that GenABEL's creator, Yurii Aulchenko, released another package called ProbABEL for genome-wide association of imputed data. ProbABEL can perform imputation analyzing quantitative, binary, and survival outcomes while taking imputation uncertainty into account.
BMC Bioinformatics - ProbABEL package for genome-wide association analysis of imputed data
GenABEL homepage
GenABEL tutorial and reference manual
ProbABEL manual
Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.
The GenABEL tutorial link seems to have died, together with the original website. Do you know where else one might find a copy?
ReplyDeleteHmm, seems to be working now. Here's a direct link to the manual and the tutorial hosted here just in case the site goes down again.
ReplyDeleteWe tried to convert genotypes for genotyped snps not in Hapmap and not imputed to MACH output format (then integrate the data with imputed snps). When testing on MACH format data for these snps, we kept getting error like 'phenofile and dosefile did not match at line 3 (MN0003 != MN0004)', while there is not problem with order id's. Anything else could cause this error? Thanks!
ReplyDeleteIs there anyway to adapt the output from IMPUTE2 for analysis using ProbAbel?
ReplyDeleteDo you know which R package can check Mendelian Error for GWAW data?
ReplyDeleteImporting my data (phenotype and SNP genotype) into GenABEL was a 'BIG' and problematic for me. Can you show an easy way to do it?
ReplyDeleteCheers,
Importing my data (phenotype and SNP genotype) into GenABEL was a 'BIG' and problematic task for me. Can you show an easy way to do it?
ReplyDeleteIs there any way to simulate SNP data?
ReplyDelete