separateXMLDataByExpt: Convert a vector of PSI-MI 2.5 XML files into graph objects...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/psi25parser.R

Description

The function psimi25XML2Graph take a vector of XML 2.5 files from te same data source and generates a graph object based on the type of the files.

Usage

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separateXMLDataByExpt(xmlFiles, psimi25source, type = "direct", directed = TRUE, abstract = FALSE,...)

Arguments

xmlFiles

Single file name or a vector of PSI-MI 2.5 XML file names or URLs.

type

A character. Currently the user can specify to cull either "direct" interactions or "indirect" interactions.

psimi25source

Source of the PSI-MI 2.5 XML file, see psimi25Source-class

directed

Logical, whehter the returned graph object should be directed or undirected.

abstract

Logical; if TRUE, the abstract information will be appended to the graph object.

...

Other parameters passed to parsePsimi25Interaction, for example verbose=TRUE

Value

A list of psimi25Graph-class are generated indexed by the pubmedID of each bait-prey interaction. WARNING - the abstract information is obtained using the pubmed and buildPubMedAbst functions from the annotate package which warns the user that NCBI may block access to their site. The default is to not obtain the abstract for this reason.

Author(s)

Jitao David Zhang, Tony Chiang

See Also

psimi25Source-class, psimi25Graph-class, psimi25Hypergraph-class

Examples

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xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

intactxml <- file.path(xmlDir, "intact_2008_test.xml")
intactGraph <- separateXMLDataByExpt(intactxml, INTACT.PSIMI25, type="indirect")

alyst/RpsiXML documentation built on July 10, 2017, 11:46 p.m.