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ScISI (version 1.42.0)
In Silico Interactome
Description
Package to create In Silico Interactomes
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Version
1.44.0
1.42.0
1.40.0
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Version
1.42.0
License
LGPL
Maintainer
Tony Chiang
Last Published
January 1st, 1970
Functions in ScISI (1.42.0)
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checkSGN
A function to check that the protein names are all systematic gene names.
checkComplex
Function to check a list of protein complexes wrt ScISI
arp23Y2HG
A graph of ARP 2/3 containing only Y2H verified interactions
arp23Orf
Constituent members of Protein Complex Arp 2/3
arp23G
The graph of arg 2/3
cfia
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
arp23
Constituent members of Protein Complex Arp 2/3
calcGraphStats
A function to calculate the various summary statistics for Y2H induced graphs
cfiaOrf
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
compareComplex
A function to compare two bipartite graph matrices
compBijection
A recursive function that greedily handles the alignment issue
eAt2
A file containing edge attributes
createMipsMatrix
A function to create the bipartite graph incidence matrix from MIPS protein complexes
eAt
An edge attribute data file
createGODataFrame
A function to create a Dataframe from the GO protein complexes
dataS
A character matrix containing the source data for the ScISI
createYeastDataObj
Creates an object of class yeastData
createGOMatrix
A function to create the bipartite graph (BG) incidence matrix from the protein complexes parsed from the GO Database
Desc
A method to return a description of a protein complex
createMipsDataFrame
A function that creates a data frame from the MIPS Data
getMipsInfo
A function that reads the downloaded text file from the MIPS repository and generates a named list of protein complexes.
getURL
A method to return an url location of a protein complex
getGOInfo
A function that parses through the GO database; it agreps for the term "complex" and greps suffixes "-ase" and "-some" and returns nodes whose description contains such terms.
getLocOrfs
A function to obtain ORFs for the ScISI
edgeProp
A function to estimate the edge proportion of a y2h induced graph on a protein complex
egEBI16112
A graph example mapping an IntAct ID to Systematic Gene Names
gavin2mergeMG
A data file containing the pre-merged Gavin to (merged) MIPS-GO data
expStats
A data file containing the experimental statistics
getAPMSData
A function to get the estimated complexes from high throughput data determined by the package apComplex.
findSubComp
A function that looks for either equality between two complexes or complete containment of one complex in another
rmByEvi
A function that parses through each GO protein complex and removes proteins based on evidence codes.
maximizeSimilarity
A function compares two bipartite graph matrices and finds the most similar matches between the clusters
sumStats
A function to calculate some summary statistics between an two interactomes
meanDeg
A function to estimate the population mean nodal degree of a protein complex of interest
unwanted
GO terms that are parsed but not protein complexes
runAlignment
A function to establish preliminaries for the compBijection function.
krogan2mergeMGGH
A data file containing the pre-merged Krogan to the (merged) MIPS-GO-Gavin-Ho data
locScISI
A data file used to estimate the location of the complexes of the ScISI
nAt
A file containing node attributes
nAtMap
A file containing node attributes
unWantedComp
A function to manually remove protein complexes from some in silico interactome
ID
A method to return the ID of a protein complex
xtraGO
A character vector of hand selected GO protein complexes
mergeBGMat
A function that merges two bipartite graph (BG) incidence matrices into one.
mips2go
A data file containing the pre-merged GO to the MIPS data
JaccardCoef
A function to calculate the Jaccard similarity index between two sets
mapping2SysG
A example graph of the mapping from IntAct to Systematic Names
mappingsG
A example graph of the mapping from IntAct to Systematic Names
nonGenes
Genes found in MIPS which are not gene locus names
nucComp
A data file containing the nuclear complexes
ScISI
The In Silico Interactome for Saccharomyces cerevisiae
runCompareComplex
A function that calls all other types of comparison functions
ho2mergeMGG
A data file containing the pre-merged Ho to the (merged) MIPS-GO-Gavin data
graphSumStats
An initiation function to generate graph statistics
redundantM
A matrix of redundant complex summary statistics
recCompSize
A function that records the relative sizes of complex C-i from one bipartite graph with complex K-j from a different bipartite graph.
yeastData-class
Class "yeastData"
xtraGONodes
A function to check manually curated GO nodes
ScISI2html
A function that generates an html page for the GO and MIPs protein complexes
subCompM
A matrix of sub-complex summary statistics