rags2ridges: kegg.target – R documentation

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kegg.target

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. `"hsa:3988"` ("`<organism>:<Entrez id>`"). It can however also be just the Entrez id with or without the post-fixed `"_at"` and then the specified `organism` will be assumed.
`kegg.id`	A `character` giving the KEGG ID, e.g. `"map04210"`, `"map04064"`, or `"map04115"`.
`method`	The method for estimating the non-zero entries moralized graph of the KEGG topology. Currently, only `"linreg"` is implemented.
`organism`	A `character` giving the organism, the default is `"hsa"` (homo-sapiens).
`graph`	A `graphNEL` object specifying the topology of the pathway. Can be used to avoid repeatedly downloading the information.

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 <cf.peeters@vumc.nl>, Wessel N. van Wieringen

References

https://www.genome.jp/kegg/

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)

rags2ridges

Ridge Estimation of Precision Matrices from High-Dimensional Data

v2.2.4

GPL (>= 2)

Authors

Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]

Initial release