qtlnet (version 1.5.4)

write.qtlnet: write qtlnet as text file

Description

Write resulting graph as text file

Usage

write.qtlnet(x, filename, edges, loci.list, include.qtl = TRUE,
    est.list, include.est = TRUE,
    digits = 3, col.names = TRUE, …)

Arguments

x

Object of class qtlnet.

filename

Character string with name of text file (usually ends in .txt).

edges

Data frame with first two columns being cause and effect directed phenotype pairs. Typically determined as averaged.net element from call to summary.qtlnet.

loci.list

List of character names of loci by phenotype. Typically determined by call to loci.qtlnet.

include.qtl

Include QTL in graph if TRUE and loci.list is not NULL.

est.list

List of estimates from internal est.qtlnet?

include.est

Include estimate if TRUE.

digits

Number of significant digits for width.

col.names

Character vector of column names.

…

Additional arguments passed to called routines.

Value

Invisibly returns data frame that corresponds to saved file.

Details

Simple write of causal network, for instance to use with Cytoscape.

References

Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann Appl Statist 4: 320-339. http://www.stat.wisc.edu/~yandell/doc/2010/92.AnnApplStat.pdf

See Also

igraph.qtlnet

Examples

# NOT RUN {
write.qtlnet(Pscdbp.qtlnet, "Pscdbp.txt")
# }