ctl (version 1.0.0-2)

CTLsignificant: CTLsignificant - Get all significant interactions from a genome-wide CTLscan

Description

Get all significant interactions from a genome-wide CTLscan.

Usage

CTLsignificant(CTLobject, significance = 0.05, what = c("names","ids"))

Arguments

CTLobject

An object of class "CTLobject", as output by CTLscan.

significance

Significance threshold to set a genome wide False Discovery Rate (FDR).

what

Return trait and marker names or column numbers (for indexing).

Value

A matrix significant CTL interactions with 4 columns: trait, marker, trait, lod

Details

TODO

References

TODO

Examples

# NOT RUN {
  library(ctl)
  data(ath.result)
  all_interactions <- CTLsignificant(ath.result)
  all_interactions[1:10, ]
  trait1_interactions <- CTLsignificant(ath.result[[1]])
  trait1_interactions
# }