ctl.regions: CTLregions - Get all significant interactions from a...

In ctl: Correlated Trait Locus Mapping

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)

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.

Details

TODO

Value

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

Note

TODO

Author(s)

Danny Arends [e-mail]
Maintainer: Danny Arends [e-mail]

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)

ctl documentation built on Nov. 27, 2023, 5:09 p.m.