## ----style-knitr, eval=TRUE, echo = FALSE, results = 'asis', warning=FALSE---- suppressPackageStartupMessages({ library("Path2PPI") }) BiocStyle::markdown() ## ----------------------------------------------------------------------------- data(ai) #Load test data set ls() #"ai" contains six data objects ## ----------------------------------------------------------------------------- human.ai.proteins yeast.ai.proteins ## ----echo=FALSE--------------------------------------------------------------- names(human.ai.proteins) ## ----eval=FALSE--------------------------------------------------------------- # str(human.ai.irefindex) # str(yeast.ai.irefindex) ## ----------------------------------------------------------------------------- head(pa2yeast.ai.homologs) head(pa2human.ai.homologs) ## ----------------------------------------------------------------------------- ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145") ## ----------------------------------------------------------------------------- ppi ## ----------------------------------------------------------------------------- ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins, human.ai.irefindex, pa2human.ai.homologs) ## ----------------------------------------------------------------------------- ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", yeast.ai.proteins, yeast.ai.irefindex, pa2yeast.ai.homologs) ## ----------------------------------------------------------------------------- showReferences(ppi) ## ----------------------------------------------------------------------------- interactions <- showReferences(ppi, species="9606", returnValue="interactions") head(interactions) ## ----------------------------------------------------------------------------- ppi <- predictPPI(ppi,h.range=c(1e-60,1e-20)) ## ----------------------------------------------------------------------------- ppi #show(ppi) ## ----------------------------------------------------------------------------- set.seed(12) #Set random seed coordinates <- plot(ppi, return.coordinates=TRUE) ## ----------------------------------------------------------------------------- plot(ppi,multiple.edges=TRUE,vertices.coordinates=coordinates) ## ----------------------------------------------------------------------------- set.seed(40) target.labels<-c("B2AE79"="PaTOR","B2AXK6"="PaATG1", "B2AUW3"="PaATG17","B2AM44"="PaATG11", "B2AQV0"="PaATG13","B2B5M3"="PaVAC8") species.colors <- c("5145"="red","9606"="blue","559292"="green") plot(ppi,type="hybrid",species.colors=species.colors, protein.labels=target.labels) ## ----------------------------------------------------------------------------- showInteraction(ppi,interaction=c("B2AT71","B2AE79")) ## ----------------------------------------------------------------------------- showInteraction(ppi,interaction=c("B2AT71","B2AE79"),mode="detailed", verbose=FALSE) ## ----------------------------------------------------------------------------- ref.interaction <- showInteraction(ppi,interaction=c("B2AT71","B2AE79"), mode="references.detailed",verbose=FALSE) ## ----------------------------------------------------------------------------- ref.interaction[ref.interaction$irigid=="742389", c("author","pmids","sourcedb")] ## ----------------------------------------------------------------------------- my.ppi <- getPPI(ppi) my.ppi ## ----------------------------------------------------------------------------- my.hybrid <- getHybridNetwork(ppi) my.hybrid ## ----sessionInfo, print=TRUE, eval=TRUE--------------------------------------- sessionInfo()