I'm conducting a meta-analysis on two genome wide association studies (GWAS), each consisting of 150 SNPs, for which I computed summary statistics for association.
I'm using the R package meta and the function metagen
.
It seems to me that this function is able to combine studies but on single measurement effect (I have 150), one for each study.
For example, I may have 3 SNPs on each study
STUDY SNP OR SE
GWAS_A rs694739 0.6691 0.07588
GWAS_A rs9858968 0.1091 0.01588
GWAS_A rs1529267 0.9291 0.02588
GWAS_B rs694739 0.6128 0.37344
GWAS_B rs9858968 0.0332 0.27344
GWAS_B rs1529267 0.3481 0.81284
so I would like an output in a table format (e.g., as in PLINK), with 3 rows and the corresponding pooling statistics.
I know I could manage it with for
loops or by grouping with the by
function on the summary output of metagen
,
but I wonder whether there is another R package/function to easily accomplish this.