check.merge: Check if snp groups can be combined

Description Usage Arguments Details Value Author(s)

Description

Check if SNP groups can be combined.

Usage

1
check.merge(d, test.groups)

Arguments

d

object of class snpmod

test.groups

list of character vectors, each vector giving the SNPs that comprise one group

Details

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.

Value

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

Author(s)

Chris Wallace


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