Post by ib on Jun 17, 2016 15:36:29 GMT
Dear all,
I am new to conditional analysis and I could not find any answer or thread regarding my questions in the forum. I have summary statistic data for a large GWAS analysis and want to test whether SNPs within a locus are independently associated with my trait. I have two questions regarding the analysis;
1. I ran the gcta-cojo slct analysis on my meta analysis data using individual data from a subset of this study as the bfile. Will this inflate my analysis? I do not have gwas data that is not also in the meta analysis.
2. The columns in the .jma.cojo file of the joint analysis, how do I interpret these? Given I have a Meta analysis file with 5 SNPs, and 3 of these are identified as independent, how is the bJ calculated? Of which SNPs is it the joint effect?
Thanks in advance
ingrid
I am new to conditional analysis and I could not find any answer or thread regarding my questions in the forum. I have summary statistic data for a large GWAS analysis and want to test whether SNPs within a locus are independently associated with my trait. I have two questions regarding the analysis;
1. I ran the gcta-cojo slct analysis on my meta analysis data using individual data from a subset of this study as the bfile. Will this inflate my analysis? I do not have gwas data that is not also in the meta analysis.
2. The columns in the .jma.cojo file of the joint analysis, how do I interpret these? Given I have a Meta analysis file with 5 SNPs, and 3 of these are identified as independent, how is the bJ calculated? Of which SNPs is it the joint effect?
Thanks in advance
ingrid
