Desc
(Package: ScISI) :
A method to return a description of a protein complex
The Desc method takes in the protein complex name of a bi-partite graph incidence matrix (usually an ad hoc name) and returns a description of that protein complex.
● Data Source:
BioConductor
● Keywords: classes
● Alias: Desc, Desc,yeastData,character-method
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ID
(Package: ScISI) :
A method to return the ID of a protein complex
The ID method takes in the protein complex name of a bi-partite graph incidence matrix (usually an ad hoc name) and returns its MIPS, GO, etc id. The object to be referenced is an instance of the class yeastData.
● Data Source:
BioConductor
● Keywords: classes
● Alias: ID, ID,yeastData,character-method
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JaccardCoef
(Package: ScISI) :
A function to calculate the Jaccard similarity index between two sets
The JaccardCoef function takes the return values of compareComplex function and calculates, for each pair of complexes C-i and K-j (where C-i is in first bipartite graph matrix and K-j is second), the similarity coefficient of Jaccard.
● Data Source:
BioConductor
● Keywords: datagen
● Alias: JaccardCoef
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ScISI2html
(Package: ScISI) :
A function that generates an html page for the GO and MIPs
This function takes a vector or url's and a vector of the protein complex description names (known names of the protein complexes) and creates an html file that lets the user link to each of the protein complex description site based on the particular url.
● Data Source:
BioConductor
● Keywords: datagen
● Alias: ScISI2html
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calcGraphStats
(Package: ScISI) :
A function to calculate the various summary statistics for Y2H
This function takes a putative protein complex (given by comp) and a list of bait to prey associations, and from these two data-sets computes various summary statistics on the induced Y2H graph which include: edge proportion of sampled nodes (baits to prey); estimated population mean nodal degree; proportion of sampled baits with hits to baits with no hits; the average out degree of baits; the proteins (bait and prey) which are not isolated; the number of connected components to the y2h graph, etc.
● Data Source:
BioConductor
● Keywords: datagen
● Alias: calcGraphStats
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checkComplex
(Package: ScISI) :
Function to check a list of protein complexes wrt ScISI
This function takes a named list of protein complexes (where each protein complex name indexes an item of the list and each list entry is the protein composition of the complex) and an interactome (in the bi-partite matrix representation) and checks to see if each complex of the list is either in the interactome, a sub-complex of some complex(es) of the interactome, or a super-complex of some complex(es) of the interactome.
● Data Source:
BioConductor
● Keywords: datagen
● Alias: checkComplex
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checkSGN
(Package: ScISI) :
A function to check that the protein names are all systematic
This function takes the in silico interactome and checks the rownames against the names of the meta-data set org.Sc.sgdALIAS from the meta-data package org.Sc.sgd
● Data Source:
BioConductor
● Keywords: datagen
● Alias: checkSGN
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compBijection
(Package: ScISI) :
A recursive function that greedily handles the alignment issue
This function takes a matrix of similarity measures (e.g. Jaccard Index) between the TSNMat and the estMat and finds the maximal value of this matrix and records its position (i,j). Then it matches C-i to K-j and then deletes row i and colunm j creating a matrix with one less row and one less colunm. The function calls itself recursively using this smaller matrix as the new argument. It stops when there are either no rows left or no columns left or the matrix of similarity measures is reduced to a 0-matrix and breaks from the recursive loop.
● Data Source:
BioConductor
● Keywords: array, datagen
● Alias: compBijection
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compareComplex
(Package: ScISI) :
A function to compare two bipartite graph matrices
The compareComplex function takes two bipartite graph matrix representations and calculates three statistics between all pairs of complexes, C-i and K-j: (1) the intersection between C-i and K-j, (2) the proteins in C-i and not in K-j, (3) the proteins in K-j and not in C-i. These stats are later used to calculate Jaccard and Dice-Sorenson Coefficients as well as probability distributions of a protein p in a complex C.
● Data Source:
BioConductor
● Keywords: array, datagen
● Alias: compareComplex
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createGODataFrame
(Package: ScISI) :
A function to create a Dataframe from the GO protein complexes
This function takes a named list (the names are the GO ID's representing some protein complex and the list elements are character vectors consisting of the members of each particular complex) and an Bipartite Graph Incidence Matrix and creates a dataframe with three columns: complex name, GO ID, and complex description.
● Data Source:
BioConductor
● Keywords: datagen
● Alias: createGODataFrame
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