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Predict cophescan hypothesis for tested associations

Source: R/cophe_hyp_predict.R
cophe.hyp.predict.Rd

Predict cophescan hypothesis for tested associations

Usage

cophe.hyp.predict(
  cophe.res,
  grouping.vars = c("querysnp", "querytrait"),
  Hc.cutoff = 0.6,
  Hn.cutoff = 0.2
)

Arguments

cophe.res

results obtained from cophe.single, cophe.susie or cophe.multitrait or data.frame with the following columns: PP.Hn, PP.Hc, PP.Ha, querysnp, querytrait

grouping.vars

This is important for results from cophe.susie where there are multiple signals. These will be collapsed into one call. If you want to return all signals set this to a single variable eg: grouping.vars = c('querysnp')

Hc.cutoff

threshold for PP.Hc above which the associations are called Hc

Hn.cutoff

threshold for PP.Hn above which the associations are called Hn

Value

returns dataframe with posterior probabilties of Hn, Hc and Ha with the predicted hypothesis based on the provided cut.offs.

See also

cophe.single, cophe.susie, cophe.multitrait, , multitrait.simplify