ctl (version 1.0.0-0)

CTLprofiles: 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, warn=TRUE)

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.

warn

Warn when there are not enough permutations.

Value

Matrix: phenotypes x marker or phenotypes x phenotypes

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.

References

TODO

Examples

# NOT RUN {
  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")
# }