CTLprofiles {ctl}

CTLprofiles - Extract CTL interaction profiles

Description

Extract the CTL interaction profiles: phenotype x marker (p2m matrix) and phenotype x phenotype (p2p matrix) from a CTLscan.

Usage

CTLprofiles(CTLobject, against = c("markers","phenotypes"), significance = 0.05, 
verbose=FALSE)

Arguments

CTLobject

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

against

Plot the CTL against either: markers or phenotypes.

significance

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

verbose

Be verbose.

Details

These matrices can be combined with QTL information to perform de novo reconstruction of interaction networks.

The 'against' parameter is by default set to "markers" which returns a phenotype x markers matrix (p2m matrix), which should be comparible to the QTL profiles of the traits.

When the 'against' parameter is set to "phenotypes" a phenotype x phenotype matrix (p2p matrix) is returned, showing the interactions between the phenotypes.

Value

Matrix: phenotypes x marker or phenotypes x phenotypes

Note

TODO

Author(s)

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

References

TODO

Examples

  library(ctl)         # Load CTL library
  data(ath.result)     # Arabidopsis Thaliana results
  p2m_matrix <- CTLprofiles(ath.result, against="markers")
  p2p_matrix <- CTLprofiles(ath.result, against="phenotypes")