buildPCHypergraph {RpsiXML} | R Documentation |
The protein complexes can be represented by hypergraph models, with proteins as nodes and complexes as hypergraphs. This function builds protein complex hypergraph from one or more PSI-MI 2.5 files (complex mode), with the option to split the dataset by organism name or taxonomy ID of the complexes.
buildPCHypergraph(xmlFiles, psimi25source, split.by = c("none", "organismName", "taxId"), ...)
xmlFiles |
PSI-MI 2.5 files, must be of complex mode. |
psimi25source |
PSI-MI 2.5 source indicator, for example INTACT.PSIMI25 for files from IntAct database |
split.by |
The qualifier to split the dataset, |
... |
other parameters passed to |
See psimi25Hypergraph-class
for the use of resulting
hypergraphs and examples.
In case the dataset is not split (by setting the option
split.by
as none
, the result is a
psimi25Hypergraph-class
object. If the dataset was
split, a list of psimi25Hypergraph-class
is returned,
which is indexed by either the organism name or the taxonomy ID.
Jitao David Zhang <jitao_david.zhang@roche.com>
psimi25Hypergraph-class
for the use of
hypergraph objects, separateXMLDataByExpt
for similar
functionality but for interaction mode files
xmlDir <- system.file("/extdata/psi25files",package="RpsiXML") intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml.gz") pc2 <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25,split.by="organismName") pc2[2] complexes(pc2[[2]])[1:3]