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ScISI (version 1.40.0)
In Silico Interactome
Description
Package to create In Silico Interactomes
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Version
1.44.0
1.42.0
1.40.0
1.38.0
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Version
1.40.0
License
LGPL
Maintainer
Tony Chiang
Last Published
January 1st, 1970
Functions in ScISI (1.40.0)
Search functions
arp23Orf
Constituent members of Protein Complex Arp 2/3
expStats
A data file containing the experimental statistics
findSubComp
A function that looks for either equality between two complexes or complete containment of one complex in another
ID
A method to return the ID of a protein complex
nonGenes
Genes found in MIPS which are not gene locus names
JaccardCoef
A function to calculate the Jaccard similarity index between two sets
checkSGN
A function to check that the protein names are all systematic gene names.
compareComplex
A function to compare two bipartite graph matrices
dataS
A character matrix containing the source data for the ScISI
Desc
A method to return a description 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
graphSumStats
An initiation function to generate graph statistics
calcGraphStats
A function to calculate the various summary statistics for Y2H induced graphs
eAt
An edge attribute data file
eAt2
A file containing edge attributes
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
xtraGONodes
A function to check manually curated GO nodes
cfia
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
createMipsMatrix
A function to create the bipartite graph incidence matrix from MIPS protein complexes
getMipsInfo
A function that reads the downloaded text file from the MIPS repository and generates a named list of protein complexes.
createYeastDataObj
Creates an object of class yeastData
getURL
A method to return an url location of a protein complex
mapping2SysG
A example graph of the mapping from IntAct to Systematic Names
mappingsG
A example graph of the mapping from IntAct to Systematic Names
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.
unWantedComp
A function to manually remove protein complexes from some in silico interactome
xtraGO
A character vector of hand selected GO protein complexes
ho2mergeMGG
A data file containing the pre-merged Ho to the (merged) MIPS-GO-Gavin data
runAlignment
A function to establish preliminaries for the compBijection function.
rmByEvi
A function that parses through each GO protein complex and removes proteins based on evidence codes.
ScISI2html
A function that generates an html page for the GO and MIPs protein complexes
subCompM
A matrix of sub-complex summary statistics
compBijection
A recursive function that greedily handles the alignment issue
arp23Y2HG
A graph of ARP 2/3 containing only Y2H verified interactions
createGODataFrame
A function to create a Dataframe from the GO protein complexes
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
yeastData-class
Class "yeastData"
createGOMatrix
A function to create the bipartite graph (BG) incidence matrix from the protein complexes parsed from the GO Database
checkComplex
Function to check a list of protein complexes wrt ScISI
cfiaOrf
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
gavin2mergeMG
A data file containing the pre-merged Gavin to (merged) MIPS-GO data
createMipsDataFrame
A function that creates a data frame from the MIPS Data
getAPMSData
A function to get the estimated complexes from high throughput data determined by the package apComplex.
nAt
A file containing node attributes
sumStats
A function to calculate some summary statistics between an two interactomes
nAtMap
A file containing node attributes
unwanted
GO terms that are parsed but not protein complexes
arp23
Constituent members of Protein Complex Arp 2/3
arp23G
The graph of arg 2/3
egEBI16112
A graph example mapping an IntAct ID to Systematic Gene Names
maximizeSimilarity
A function compares two bipartite graph matrices and finds the most similar matches between the clusters
edgeProp
A function to estimate the edge proportion of a y2h induced graph on a protein complex
mergeBGMat
A function that merges two bipartite graph (BG) incidence matrices into one.
meanDeg
A function to estimate the population mean nodal degree of a protein complex of interest
mips2go
A data file containing the pre-merged GO to the MIPS data