CTLnetwork {ctl}

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:

• ctlnet<FILE>.sif - Shows CTL connections from Trait to Marker with edge descriptions

• ctlnet<FILE>.nodes - Attributes of the nodes (Traits and Genetic markers) nodes to this file can be used to either color chromosomes, or add chromosome locations.

Value

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

• TRAIT1 - Trait ID of the origin trait

• MARKER - Marker ID at which the CTL was found

• TRAIT2 - Trait ID of the target trait

• LOD_C - LOD score of the CTL interaction

• CAUSAL - Type of edge determined by QTL LOD-drop:

  • NA - CTL/QTL for TRAIT1 and/or TRAIT2 not found

  • -1 - TRAIT1 is DOWNSTREAM of TRAIT2

  • 0 - UNDETERMINED Edge

  • 1 - TRAIT1 is UPSTREAM of TRAIT2

• LOD_T1 - QTL LOD-score of TRAIT1 at MARKER

• LOD_T2 - QTL LOD-score of TRAIT2 at MARKER

Note

TODO

Author(s)

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

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)