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ENVISIONQuery (version 1.20.0)

Retrieval from the ENVISION bioinformatics data portal into R

Description

Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal

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Version

Version

1.20.0

License

GPL-2

Maintainer

Alex Lisovich Roger Day day01pittedu

Last Published

February 15th, 2017

Functions in ENVISIONQuery (1.20.0)

ENVISIONQuery.loop

Perform queries in chunks to comply with potential limitations...
getIdMatchInfo

Retrieve the set of match pairs from the 'Entry' node of the Enfin xml document.
formatReactome

Convert the EnXML PICR service results file into the protein interaction data frame...
formatIntact

Convert the EnXML IntAct service results file into the protein interaction data frame...
formatIdMap

Convert the Enfin xml ID conversion results file into the pair match data frame...
registerServices

Register available Envision services...
getServices

Get available services...
getServiceClient

Get the Web Service client finction handler for a given tool...
ENVISIONQuery

Launch a query against Envision, a web online query system...
getMerger

Get the merging function for a given tool.
getIdEntries

Retrieve a set of all ID entries...
getServiceOptions

Get default service options.
jgetOptions

Convert options list into the character vector.
getFormatter

Get the formatting function for a given tool...
getPicrMatchInfo

Retrieve PICR match info from the 'Entry' node of the Enfin xml document.
getServiceNames

Get the names of available Envision services...
getPositiveResultSetIDs

Retrieve a set of positive query result references from the 'Entry' node of the Enfin xml document.
ENVISIONQuery.chunk

Retrieves a set of unique matches for a given ID list.
mergeMatchRows

Merge a set of rows with non-unique values in a given set of columns.
formatPicr

Convert the EnXML PICR service results file into the protein interaction data frame...
getReactomeMatchInfo

Retrieve Reactome pathway match info from the 'Entry' node of the Enfin xml document.
getInputTypes

Get the list of available input types for a given tool.
mergeFrameList

Merges the data frames representing the partial query results into a single data frame.
toChunks

Convert the ID set into the list of ID subsets.
getTool

Get the tool handler of a given service using the tool name...
getInputIdEntries

Retrieve a set of input ID entries...
getService

Get the service handler using it's name...
ENVISIONQuery-package

ENVISIONQuery.
progressMsg

Display the task progress message.
getIntactMatchInfo

Retrieve IntAct match info from the 'Entry' node of the Enfin xml document.
ENVISIONServices

Registry of available Envision services...
getToolNames

Get the names of available tools for a given Envision service...