ScISI: In Silico Interactome
Version 1.48.0

Package to create In Silico Interactomes

Browse man pages Browse package API and functions Browse package files

AuthorTony Chiang <tchiang@fhcrc.org>
Bioconductor views DecisionTree GraphAndNetwork NetworkInference Proteomics
Date of publicationNone
MaintainerTony Chiang <tchiang@fhcrc.org>
LicenseLGPL
Version1.48.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ScISI")

Man pages

arp23: Constituent members of Protein Complex Arp 2/3
arp23G: The graph of arg 2/3
arp23Orf: Constituent members of Protein Complex Arp 2/3
arp23Y2HG: A graph of ARP 2/3 containing only Y2H verified interactions
calcGraphStats: A function to calculate the various summary statistics for...
cfia: Constituent members of Protein Complex Cleavage Factor IA...
cfiaOrf: Constituent members of Protein Complex Cleavage Factor IA...
checkComplex: Function to check a list of protein complexes wrt ScISI
checkSGN: A function to check that the protein names are all systematic...
compareComplex: A function to compare two bipartite graph matrices
compBijection: A recursive function that greedily handles the alignment...
createGODataFrame: A function to create a Dataframe from the GO protein...
createGOMatrix: A function to create the bipartite graph (BG) incidence...
createMipsDataFrame: A function that creates a data frame from the MIPS Data
createMipsMatrix: A function to create the bipartite graph incidence matrix...
createYeastDataObj: Creates an object of class yeastData
dataS: A character matrix containing the source data for the ScISI
Desc-methods: A method to return a description of a protein complex
eAt: An edge attribute data file
eAt2: A file containing edge attributes
edgeProp: A function to estimate the edge proportion of a y2h induced...
egEBI16112: A graph example mapping an IntAct ID to Systematic Gene Names
expStats: A data file containing the experimental statistics
findSubComp: A function that looks for either equality between two...
gavin2mergeMG: A data file containing the pre-merged Gavin to (merged)...
getAPMSData: A function to get the estimated complexes from high...
getGOInfo: A function that parses through the GO database; it agreps for...
getLocOrfs: A function to obtain ORFs for the ScISI
getMipsInfo: A function that reads the downloaded text file from the MIPS...
getURL-methods: A method to return an url location of a protein complex
graphSumStats: An initiation function to generate graph statistics
ho2mergeMGG: A data file containing the pre-merged Ho to the (merged)...
ID-methods: A method to return the ID of a protein complex
JaccardCoef: A function to calculate the Jaccard similarity index between...
krogan2mergeMGGH: A data file containing the pre-merged Krogan to the (merged)...
locScISI: A data file used to estimate the location of the complexes of...
mapping2SysG: A example graph of the mapping from IntAct to Systematic...
mappingsG: A example graph of the mapping from IntAct to Systematic...
maximizeSimilarity: A function compares two bipartite graph matrices and finds...
meanDeg: A function to estimate the population mean nodal degree of a...
mergeBGMat: A function that merges two bipartite graph (BG) incidence...
mips2go: A data file containing the pre-merged GO to the MIPS data
nAt: A file containing node attributes
nAtMap: A file containing node attributes
nonGenes: Genes found in MIPS which are not gene locus names
nucComp: A data file containing the nuclear complexes
recCompSize: A function that records the relative sizes of complex C-i...
redundantM: A matrix of redundant complex summary statistics
rmByEvi: A function that parses through each GO protein complex and...
runAlignment: A function to establish preliminaries for the compBijection...
runCompareComplex: A function that calls all other types of comparison functions
ScISI: The In Silico Interactome for Saccharomyces cerevisiae
ScISI2html: A function that generates an html page for the GO and MIPs...
subCompM: A matrix of sub-complex summary statistics
sumStats: A function to calculate some summary statistics between an...
unwanted: GO terms that are parsed but not protein complexes
unWantedComp: A function to manually remove protein complexes from some in...
xtraGO: A character vector of hand selected GO protein complexes
xtraGONodes: A function to check manually curated GO nodes
yeastData-class: Class "yeastData"

Functions

Desc Man page
Desc,yeastData,character-method Man page
ID Man page
ID,yeastData,character-method Man page
JaccardCoef Man page Source code
ScISI Man page
ScISI2html Man page Source code
ScISIC Man page
ScISIverified Man page
arp23 Man page
arp23G Man page
arp23Orf Man page
arp23Y2HG Man page
calcGraphStats Man page Source code
cfia Man page
cfiaOrf Man page
checkComplex Man page Source code
checkSGN Man page Source code
compBijection Man page Source code
compareComplex Man page Source code
createGODataFrame Man page Source code
createGOMatrix Man page Source code
createMipsDataFrame Man page Source code
createMipsMatrix Man page Source code
createYeastDataObj Man page Source code
dataS Man page
eAt Man page
eAt2 Man page
edgeProp Man page Source code
egEBI16112 Man page
expStats Man page
findSubComp Man page Source code
gavin2mergeMG Man page
getAPMSData Man page Source code
getGOInfo Man page Source code
getLocOrfs Man page Source code
getMipsInfo Man page Source code
getURL Man page
getURL,yeastData,character-method Man page
graphSumStats Man page Source code
ho2mergeMGG Man page
krogan2mergeMGGH Man page
locScISI Man page
mapping2SysG Man page
mappingsG Man page
maximizeSimilarity Man page Source code
meanDeg Man page Source code
mergeBGMat Man page Source code
mips2go Man page
nAt Man page
nAtMap Man page
nonGenes Man page
nucComp Man page
recCompSize Man page Source code
redundantM Man page
rmByEvi Man page Source code
runAlignment Man page Source code
runCompareComplex Man page Source code
subCompM Man page
sumStats Man page Source code
unWantedComp Man page Source code
unwanted Man page
xtraGO Man page
xtraGONodes Man page Source code
yeastData Man page
yeastData-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/JaccardCoef.R
R/ScISI2html.R
R/calcGraphStats.R
R/checkComplex.R
R/checkSGN.R
R/compBijection.R
R/compareComplex.R
R/createGODataFrame.R
R/createGOMatrix.R
R/createMipsDataFrame.R
R/createMipsMatrix.R
R/createYeastDataObj.R
R/edgeProp.R
R/findSubComp.R
R/getAPMSData.R
R/getGOInfo.R
R/getLocOrfs.R
R/getMipsInfo.R
R/graphSumStats.R
R/initClasses.R
R/maximizeSimilarity.R
R/meanDeg.R
R/mergeBGMat.R
R/recCompSize.R
R/rmByEvi.R
R/runAlignment.R
R/runCompareComplex.R
R/sumStats.R
R/unWantedComp.R
R/xtraGONodes.R
build
build/vignette.rds
data
data/ScISI.rda
data/ScISIC.rda
data/ScISIverified.R
data/ScISIverified.rda
data/arp23.rda
data/arp23G.rda
data/arp23Orf.rda
data/arp23Y2HG.rda
data/cfia.rda
data/cfiaOrf.rda
data/dataS.rda
data/eAt.rda
data/eAt2.rda
data/egEBI16112.rda
data/expStats.rda
data/gavin2mergeMG.rda
data/ho2mergeMGG.rda
data/krogan2mergeMGGH.rda
data/locScISI.rda
data/mapping2SysG.rda
data/mappingsG.rda
data/mips2go.rda
data/nAt.rda
data/nAtMap.rda
data/nonGenes.rda
data/nucComp.rda
data/redundantM.rda
data/subCompM.rda
data/unwanted.rda
data/xtraGO.rda
inst
inst/Scripts
inst/Scripts/C1G.rda
inst/Scripts/Comments
inst/Scripts/Comments2
inst/Scripts/ckCrystStruct.R
inst/Scripts/createMipsY2HMatrix.R
inst/Scripts/createScISI.R
inst/Scripts/createScISIC.R
inst/Scripts/creatingScISI.Rnw
inst/Scripts/estGavin02.R
inst/Scripts/estGavin06.R
inst/Scripts/estHo02.R
inst/Scripts/estKrogan04.R
inst/Scripts/estKrogan06.R
inst/Scripts/estimateComp.R
inst/Scripts/getLocOrfs.Rnw
inst/Scripts/getMipsY2HInfo.R
inst/Scripts/graphStatistics.Rnw
inst/Scripts/notesMips.R
inst/Scripts/notesOtherComps
inst/Scripts/sim.R
inst/Scripts/test1.R
inst/TODO
inst/TODO/CrystalStructures
inst/TODO/Validate
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/extdata
inst/extdata/Arp2_3_complex.jpg
inst/extdata/Arp2_3_complex.png
inst/extdata/PPI_141105.tab.gz
inst/extdata/complexcat.scheme
inst/extdata/complexcat.scheme.edit
inst/extdata/complexcat_data_14112005.gz
inst/extdata/complexcat_data_18052006.gz
inst/extdata/complexcat_data_20062005.gz
inst/extdata/evidencecat.scheme
inst/extdata/graphs
inst/extdata/graphs/Readme
inst/extdata/graphs/arp23AM.rda
inst/extdata/graphs/arp23BP.rda
inst/extdata/graphs/arp23BPG.rda
inst/extdata/graphs/arp23CMG.rda
inst/extdata/graphs/arp23CMM.rda
inst/extdata/graphs/arp23G.rda
inst/extdata/graphs/cfiaAM.rda
inst/extdata/graphs/cfiaCMG.rda
inst/extdata/graphs/cfiaCMM.rda
inst/extdata/graphs/cfiaG.rda
inst/extdata/graphs/ppi1.rda
inst/extdata/graphs/ppi1G.rda
inst/extdata/graphs/ppi2.rda
inst/extdata/graphs/ppi2G.rda
inst/extdata/localization
inst/extdata/localization/allOrfData.txt
inst/extdata/pathway
inst/extdata/pathway/biochemical_pathways.tab
inst/extdata/pathway/keggM.rda
inst/extdata/pathway/sgdPathM.rda
inst/extdata/protein_network_large.jpg
man
man/Desc-methods.Rd
man/ID-methods.Rd
man/JaccardCoef.Rd
man/ScISI.Rd
man/ScISI2html.Rd
man/arp23.Rd
man/arp23G.Rd
man/arp23Orf.Rd
man/arp23Y2HG.Rd
man/calcGraphStats.Rd
man/cfia.Rd
man/cfiaOrf.Rd
man/checkComplex.Rd
man/checkSGN.Rd
man/compBijection.Rd
man/compareComplex.Rd
man/createGODataFrame.Rd
man/createGOMatrix.Rd
man/createMipsDataFrame.Rd
man/createMipsMatrix.Rd
man/createYeastDataObj.Rd
man/dataS.Rd
man/eAt.Rd
man/eAt2.Rd
man/edgeProp.Rd
man/egEBI16112.Rd
man/expStats.Rd
man/findSubComp.Rd
man/gavin2mergeMG.Rd
man/getAPMSData.Rd
man/getGOInfo.Rd
man/getLocOrfs.Rd
man/getMipsInfo.Rd
man/getURL-methods.Rd
man/graphSumStats.Rd
man/ho2mergeMGG.Rd
man/krogan2mergeMGGH.Rd
man/locScISI.Rd
man/mapping2SysG.Rd
man/mappingsG.Rd
man/maximizeSimilarity.Rd
man/meanDeg.Rd
man/mergeBGMat.Rd
man/mips2go.Rd
man/nAt.Rd
man/nAtMap.Rd
man/nonGenes.Rd
man/nucComp.Rd
man/recCompSize.Rd
man/redundantM.Rd
man/rmByEvi.Rd
man/runAlignment.Rd
man/runCompareComplex.Rd
man/subCompM.Rd
man/sumStats.Rd
man/unWantedComp.Rd
man/unwanted.Rd
man/xtraGO.Rd
man/xtraGONodes.Rd
man/yeastData-class.Rd
vignettes
vignettes/bioc.bib
vignettes/vignette.Rnw
ScISI documentation built on May 20, 2017, 9:25 p.m.