check.merge: Check if snp groups can be combined
In chr1swallace/GUESSFM: Using GUESS for Fine Mapping

Description Usage Arguments Details Value Author(s)

Check if SNP groups can be combined.

1	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

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.

shows the posterior probability of models containing exactly one, any, or all of the SNPs.

Chris Wallace

chr1swallace/GUESSFM documentation built on May 13, 2019, 6:17 p.m.