collectIntactData {y2hStat}R Documentation

A function that parses the Intact repository for bait to prey affiliation

Description

This function is the parsing function for the Intact downloaded data-sets.

Usage

collectIntactData(intactID)

Arguments

intactID A character vector of the Intact ID's that reference the particular experiment needed to be parsed.

Details

The collectIntactData is a general function that reads a downloaded (and organized) xml file, and gathers information for the set of desired experiments.

Value

numBaits The number of distinct baits over all experiments
numPreys The number of distinct preys over all experiments
allBaits A character vector of all distince baits over all experiments
allPreys A character vector of all distinct preys over all experiments
intactID The intact ID's of all the experiments
indexSetAll A list of lists. Each element of the top list corresponds to a particular experiment; the elements of these sub-lists are character vectors. The character vectors will always carry the bait protein in the first element and all of the preys that particular bait has found as the rest of the elements to the vector. Note that the multiplicity is not guarenteed to be unity.
baitsSystematic A character vector with a number of baits mapped to their systematic names
preysSystematic A character vector with a number of preys mapped to their systematic names
shortL A character vector listing the first author of each experiment.
tableList The organized xml file parsed by the function.

Author(s)

T Chiang

References

http://www.ebi.ac.uk/intact

Examples


  inTactData <- collectIntactData(c("EBI-375746", "EBI-531419",
                                    "EBI-295760", "EBI-698096"))


[Package y2hStat version 1.2.0 Index]