cophe.hyp.predict: Predict cophescan hypothesis for tested associations

In ichcha-m/cophescan: Adaptation of the Coloc Method for PheWAS

Predict cophescan hypothesis for tested associations

Description

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

ichcha-m/cophescan documentation built on June 16, 2024, 1:39 a.m.