kegg.target {rags2ridges} | R Documentation |
Construct target matrix from KEGG
Description
Construct a target matrix by combining topology information from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and pilot data.
Usage
kegg.target(
Y,
kegg.id,
method = "linreg",
organism = "hsa",
graph = getKEGGPathway(kegg.id)$graph
)
Arguments
Y |
The complete observation matrix of observations with variables in
columns. The column names should be on the form e.g. |
kegg.id |
A |
method |
The method for estimating the non-zero entries moralized graph
of the KEGG topology. Currently, only |
organism |
A |
graph |
A |
Details
The function estimates the precision matrix based on the topology given by the KEGG database. Requires a connection to the internet.
Value
Returns a target matrix
with size depending on the
kegg.id
.
Note
It is currently nessesary to require("KEGGgraph")
(or
require("KEGGgraph")
) due to a bug in KEGGgraph.
Author(s)
Anders Ellern Bilgrau, Carel F.W. Peeters <carel.peeters@wur.nl>, Wessel N. van Wieringen
References
See Also
getKEGGPathway
, default.target
, and
default.target.fused
Examples
## Not run:
if (require("KEGGgraph")) {
kegg.g <- getKEGGPathway("map04115")$graph
# Create some toy data with the correct names
Y <- createS(n = 10, p = numNodes(kegg.g), dataset = TRUE)
colnames(Y) <- nodes(kegg.g)
T <- kegg.target(Y, "map04115")
print(T[1:10, 1:10])
}
## End(Not run)