CTLnetwork {ctl}R Documentation

CTLnetwork - Interaction network from a genome-wide CTLscan of multiple traits

Description

Create a file containing the interaction network from a genome-wide CTLscan of multiple traits.

Usage

CTLnetwork(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, 
what = c("names", "ids"), short = FALSE, add.qtls = FALSE, file = "", 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 (only significant markers will be annotated).

significance

Significance threshold for a genome wide false discovery rate (FDR).

LODdrop

Drop in LOD score needed before we assign an edge type.

what

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

short

Edges are markers when TRUE, otherwise markers are nodes (default).

add.qtls

Should marker QTL trait interactions be added to the generated sif network file, QTLs are included when they are above -log10(significance/n.markers).

file

A connection, or a character string naming the file to print to. If "" (the default), CTLnetwork prints to the standard output connection, the console unless redirected by sink.

verbose

Be verbose.

Details

Outputs a sif network file, and a node attribute file:

Value

A matrix with significant CTL interactions and information in 5 Columns:

Note

TODO

Author(s)

Danny Arends Danny.Arends@gmail.com
Maintainer: Danny Arends Danny.Arends@gmail.com

References

TODO

Examples

  library(ctl)
  data(ath.result)       # Arabidopsis Thaliana results
  data(ath.metabolites)  # Arabidopsis Thaliana data set

  ctls <- CTLnetwork(ath.result, significance = 0.1)
  op <- par(mfrow = c(2,1))
  plot(ctls)
  ctl.lineplot(ath.result, ath.metab$map, significance=0.1)

[Package ctl version 1.0.0-7 Index]