Description Usage Arguments Details Value Note Author(s) See Also Examples
Retrieves a graph from a datasource converting it to an igraph
object as well as retrieving accompanying annotation.
1 | get.protein.protein.graph(db.con, param.obj, get.annotation = TRUE, on.symbol.protein.dup="remove.dup")
|
db.con |
An object inheriting from |
param.obj |
A |
get.annotation |
A |
on.symbol.protein.dup |
This controls how duplicated proteins are handled in this program. Currently, the default and only (but not optimal) option is "remove.dup". This removes the duplicate entries keeping only one for each protein. |
The graph has to be in form usable by graph.data.frame
function in the igraph
package. The graph will be retrieved using the getMatrixQuery
method of priorDbParams
.
If get.annotation
is TRUE, the getAnnotQuery
method will be used to retrieve annotation. If nodeWeightCol
is specified, then the specified values will be multiplied
with the entire set of edges for each gene and the edge scores will be modified accordingly.
An annotatedIGraph
object
Edge re-weighting through a specified nodeWeightCol
should be considered highly experimental and is subject to change.
Daniel Bottomly
graph.data.frame
, priorDbParams
, dbConnect
1 2 3 4 5 6 7 8 | if (require(HitWalkerData) && require(RSQLite))
{
data(params)
db.con <- dbConnect("SQLite", annot.db.path())
annotQuery(examp.prior.param) <- function(sample.id.list, param.obj){"SELECT * FROM annotation"}
graph.obj <- get.protein.protein.graph(db.con, examp.prior.param, get.annotation=TRUE)
## Not run: saveGraph(graph.obj, file="graph.RData")
}
|
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