separateXMLDataByExpt {Rintact}R Documentation

A function that takes a vector of IntAct XML file name locations and converts them to graph objects.

Description

The separateXMLDataByExpt function takes in a vector of XML files and generates a list of graph objects dividing the data by separately conducted experiments. If a single XML file contains k experimental datasets, then k intactGraph objects will be produced.

Usage

separateXMLDataByExpt(intactFiles, type="direct", directed=TRUE)

Arguments

intactFiles A vector of IntAct XML file name locations, i.e. either where they can be found on the local hard drive or an url to where they can be obtained
type A character. Either "direct" or "indirect" based on the ` the information that needs to be parsed.
directed A logical. User defined parameter so that the return value with either be a directed or undirected graph object.

Value

A list of intactGraph objects.

Author(s)

T Chiang

References

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository - Tony Chiang; Nianhua Li; Sandra Orchard; Samuel Kerrien; Henning Hermjakob; Robert Gentleman; Wolfgang Huber Bioinformatics 2007; doi: 10.1093/bioinformatics/btm518.

See Also

interactionEntry-class, complexEntry-class, intactXML2Graph


[Package Rintact version 1.4.0 Index]