ctl (version 1.0.0-10)

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

Description

Get all significant interactions from a genome-wide CTLscan.

Usage

CTLregions(CTLobject, mapinfo, phenocol = 1, significance = 0.05, verbose = TRUE)

Value

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

Arguments

CTLobject

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

mapinfo

The mapinfo matrix with 3 columns: "Chr" - the chromosome number, "cM" - the location of the marker in centiMorgans and the 3rd column "Mbp" - The location of the marker in Mega basepairs. If supplied the marker names (rownames) should match those in the CTLobject.

phenocol

Which phenotype column should we analyse.

significance

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

verbose

Be verbose.

Author

Danny Arends
Maintainer: Danny Arends

Details

TODO

References

TODO

Examples

  library(ctl)
  
  data(ath.metabolites)                 # Arabidopsis Thaliana data set
  data(ath.result)                      # Arabidopsis Thaliana CTL results
  regions <- CTLregions(ath.result, ath.metab$map)