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, none
specifies not to split the dataset, organismName and
taxId splits the dataset according to organism name or
taxonomy ID respectively. In the case of splitting, the results are
a list of hypergraphs indexed by respective split qualifier |
... |
other parameters passed to parsePsimi25Complex |
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 <j.zhang@dkfz.de>
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") pc2 <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25,split.by="organismName") pc2[2] complexes(pc2[[2]])[1:3]