cls.MITABDBAccess.CMITABDBAccess Class Reference

Accesses interaction data that has been stored in a specific database schema before. More...

Public Member Functions
def	Close (self)
	Close connection to the database. More...
def	Initialize (self, config, mitabConfig=None)
	Initialize and establish database connection using the parameters provided in the configuration file. More...
def	GetInteractionsByID (self, queryIds=None, targetIds=None, limit=None)
def	GetSignificanceOfInteractionOverlap (self, queryId, setIds)
	Compute likelihood ratio and p-value for the overlap of interactions annotated to the query id and the set ids. More...
def	GetStats (self)

Public Attributes
	mitabConfig
	db
	cache

Detailed Description

Accesses interaction data that has been stored in a specific database schema before.

Member Function Documentation

Close()

def cls.MITABDBAccess.CMITABDBAccess.Close

(

self

)

Close connection to the database.

GetInteractionsByID()

def cls.MITABDBAccess.CMITABDBAccess.GetInteractionsByID	(		self,
			queryIds = None,
			targetIds = None,
			limit = None
	)

     Get all the interactions that are known for the query id(s) provided.

     @param queryIds Identifiers of the queries
     @param targetIds Identifiers of the targets, optional
     @return A list of interactions

GetSignificanceOfInteractionOverlap()

def cls.MITABDBAccess.CMITABDBAccess.GetSignificanceOfInteractionOverlap	(		self,
			queryId,
			setIds
	)

Compute likelihood ratio and p-value for the overlap of interactions annotated to the query id and the set ids.

In contrast to GetInteractionsByID, this method does not return any interactions that involve queryId and setIds, but will use these to compute the significance of the overlap, considering all interactions as the background. The likelihood ratio and pvalue are computed using Fisher's exact test

Parameters

queryId	The id of the query interactors
setIds	THe ids of the interactors annotated to a certain set

Returns

A tuple containing likelihood ratio, p-value

GetStats()

def cls.MITABDBAccess.CMITABDBAccess.GetStats

(

self

)

     Returns some statistics.

     @return A dictionary containing some basic interaction information.

Initialize()

def cls.MITABDBAccess.CMITABDBAccess.Initialize	(		self,
			config,
			mitabConfig = None
	)

Initialize and establish database connection using the parameters provided in the configuration file.

Parameters

config	common.Paths.CPaths object containing database access credentials
mitabConfig	Additional parameters defining the interaction types or detection methods that should be considered.

Returns

True if all went ok. False if there was an error (issued by common.ErrorHandler).

Member Data Documentation

cache

cls.MITABDBAccess.CMITABDBAccess.cache

db

cls.MITABDBAccess.CMITABDBAccess.db

mitabConfig

cls.MITABDBAccess.CMITABDBAccess.mitabConfig

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The documentation for this class was generated from the following file:

• cls/MITABDBAccess.py