check.merge.RdCheck if SNP groups can be combined.
check.merge(d, test.groups)
| d | object of class snpmod |
|---|---|
| test.groups | list of character vectors, each vector giving the SNPs that comprise one group |
shows the posterior probability of models containing exactly one, any, or all of the SNPs.
snp.picker tries to automatically group SNPs according the r2 and the model posterior probs, but may sometimes make two separate groups when one combined group might be considered more appropriate. To check whether two groups can be combined, we need to check that SNPs from both groups are rarely included in the same models.
If the output shows that pp["all"] >> pp["any"], and the SNPs have
been shown to be in some LD, then it is likely that the groups can
be appropriately merged, using groups.merge.