inst/doc/IMMAN.R

In IMMAN: Interlog protein network reconstruction by Mapping and Mining ANalysis

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library(IMMAN)


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data(FruitFly)
data(Celegance)

subFruitFly <- as.character(FruitFly$V1)[1:10]

subCelegance <- as.character(Celegance$V1)[1:10]


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ProteinLists = list(subFruitFly, subCelegance)

List1_Species_ID = 7227    # taxonomy ID FruitFly
List2_Species_ID = 6239    # taxonomy ID Celegance

Species_IDs  = c(List1_Species_ID, List2_Species_ID)


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identityU = 30
substitutionMatrix = "BLOSUM62"
gapOpening = -8
gapExtension = -8
NetworkShrinkage = FALSE
coverage = 1
BestHit = TRUE
score_threshold = 400
STRINGversion="11"


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output = IMMAN(ProteinLists, fileNames=NULL, Species_IDs,
              identityU, substitutionMatrix,
              gapOpening, gapExtension, BestHit,
              coverage, NetworkShrinkage,
              score_threshold, STRINGversion,
              InputDirectory = getwd())


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output$IPNEdges
output$IPNNodes
output$Networks
output$Networks[[1]]
output$maps
output$maps[[2]]