RDocumentation
Moon
Learn R
Search all packages and functions
ScISI (version 1.44.0)
In Silico Interactome
Description
Package to create In Silico Interactomes
Copy Link
Copy
Link to current version
Version
Version
1.44.0
1.42.0
1.40.0
1.38.0
Down Chevron
Version
1.44.0
License
LGPL
Maintainer
Tony Chiang
Last Published
January 1st, 1970
Functions in ScISI (1.44.0)
Search functions
getAPMSData
A function to get the estimated complexes from high throughput data determined by the package apComplex.
createGOMatrix
A function to create the bipartite graph (BG) incidence matrix from the protein complexes parsed from the GO Database
createGODataFrame
A function to create a Dataframe from the GO protein complexes
ho2mergeMGG
A data file containing the pre-merged Ho to the (merged) MIPS-GO-Gavin data
eAt
An edge attribute data file
krogan2mergeMGGH
A data file containing the pre-merged Krogan to the (merged) MIPS-GO-Gavin-Ho data
Desc
A method to return a description of a protein complex
arp23Orf
Constituent members of Protein Complex Arp 2/3
nAtMap
A file containing node attributes
arp23Y2HG
A graph of ARP 2/3 containing only Y2H verified interactions
getLocOrfs
A function to obtain ORFs for the ScISI
xtraGO
A character vector of hand selected GO protein complexes
createMipsDataFrame
A function that creates a data frame from the MIPS Data
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.
createMipsMatrix
A function to create the bipartite graph incidence matrix from MIPS protein complexes
compBijection
A recursive function that greedily handles the alignment issue
xtraGONodes
A function to check manually curated GO nodes
ID
A method to return the ID of a protein complex
mergeBGMat
A function that merges two bipartite graph (BG) incidence matrices into one.
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.
eAt2
A file containing edge attributes
arp23
Constituent members of Protein Complex Arp 2/3
JaccardCoef
A function to calculate the Jaccard similarity index between two sets
calcGraphStats
A function to calculate the various summary statistics for Y2H induced graphs
unWantedComp
A function to manually remove protein complexes from some in silico interactome
cfia
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
cfiaOrf
Constituent members of Protein Complex Cleavage Factor IA (CFIA)
findSubComp
A function that looks for either equality between two complexes or complete containment of one complex in another
maximizeSimilarity
A function compares two bipartite graph matrices and finds the most similar matches between the clusters
ScISI2html
A function that generates an html page for the GO and MIPs protein complexes
checkComplex
Function to check a list of protein complexes wrt ScISI
mapping2SysG
A example graph of the mapping from IntAct to Systematic Names
createYeastDataObj
Creates an object of class yeastData
edgeProp
A function to estimate the edge proportion of a y2h induced graph on a protein complex
rmByEvi
A function that parses through each GO protein complex and removes proteins based on evidence codes.
mappingsG
A example graph of the mapping from IntAct to Systematic Names
runAlignment
A function to establish preliminaries for the compBijection function.
yeastData-class
Class "yeastData"
ScISI
The In Silico Interactome for Saccharomyces cerevisiae
mips2go
A data file containing the pre-merged GO to the MIPS data
nucComp
A data file containing the nuclear complexes
checkSGN
A function to check that the protein names are all systematic gene names.
arp23G
The graph of arg 2/3
dataS
A character matrix containing the source data for the ScISI
expStats
A data file containing the experimental statistics
nonGenes
Genes found in MIPS which are not gene locus names
graphSumStats
An initiation function to generate graph statistics
getURL
A method to return an url location of a protein complex
meanDeg
A function to estimate the population mean nodal degree of a protein complex of interest
sumStats
A function to calculate some summary statistics between an two interactomes
nAt
A file containing node attributes
subCompM
A matrix of sub-complex summary statistics
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
compareComplex
A function to compare two bipartite graph matrices
getMipsInfo
A function that reads the downloaded text file from the MIPS repository and generates a named list of protein complexes.
runCompareComplex
A function that calls all other types of comparison functions
redundantM
A matrix of redundant complex summary statistics
locScISI
A data file used to estimate the location of the complexes of the ScISI
unwanted
GO terms that are parsed but not protein complexes