Description Usage Arguments Value Author(s) References See Also Examples
The pcgen algorithm starting with a skeleton estimated using the standard pc-algorithm, based on residuals from the GBLUP.
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suffStat |
A data.frame, of which the first column is the factor G (genotype), and subsequent columns contain the traits, and optionally some QTLs. The name of the first column should be G. |
alpha |
The significance level used in each conditional independence test. Default is 0.01. |
m.max |
Maximum size of the conditioning set, in the pcgen algorithm. |
res.m.max |
Maximum size of the conditioning set, in the pc-algorithm on the residuals (used for prior screening). |
verbose |
If |
covariates |
A data.frame containing covariates, to be used in each conditional independence test. Cannot contain factors. Should be either |
fixedEdges |
A logical matrix of dimension (p+1) \times (p+1), where p is the number of traits. The first row and column refer to the node G, and subsequent rows and columns to the traits. As in the |
QTLs |
Column numbers in |
max.iter |
Maximum number of iterations in the EM-algorithm, used to fit the bivariate mixed model (when |
stop.if.significant |
If |
cov.method |
A string, specifying which method should be used to compute the GBLUP. Options are |
use.res |
If |
return.pvalues |
If |
If return.pvalues = FALSE
, the output is a graph (an object with S3 class "pcgen"
). If return.pvalues = TRUE
, the output is a list with elements gr
(the graph) and pMax
(a matrix with the p-values).
Willem Kruijer and Pariya Behrouzi. Maintainers: Willem Kruijer willem.kruijer@wur.nl and Pariya Behrouzi pariya.behrouzi@gmail.com
1. Kruijer, W., Behrouzi, P., Rodriguez-Alvarez, M. X., Wit, E. C., Mahmoudi, S. M., Yandell, B., Van Eeuwijk, F., (2018, in preparation), Reconstruction of networks with direct and indirect genetic effects.
2. Colombo, D. and Maathuis, M.H., 2014. Order-independent constraint-based causal structure learning. The Journal of Machine Learning Research, 15(1), pp.3741-3782.
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