## ----LoadPackageToDetermineVersion,echo=FALSE,message=FALSE,results='hide'---- options(width=72) knitr::opts_knit$set(width=72) set.seed(0) library(procoil, quietly=TRUE) procoilVersion <- packageDescription("procoil")$Version procoilDateRaw <- packageDescription("procoil")$Date procoilDateYear <- as.numeric(substr(procoilDateRaw, 1, 4)) procoilDateMonth <- as.numeric(substr(procoilDateRaw, 6, 7)) procoilDateDay <- as.numeric(substr(procoilDateRaw, 9, 10)) procoilDate <- paste(month.name[procoilDateMonth], " ", procoilDateDay, ", ", procoilDateYear, sep="") ## ----InstallPrOCoil,eval=FALSE------------------------------------------- ## source("http://www.bioconductor.org/biocLite.R") ## biocLite("procoil") ## ----LoadPrOCoil,eval=FALSE---------------------------------------------- ## library(procoil) ## ----PredictGCN4WildType------------------------------------------------- GCN4wt <- predict(PrOCoilModel, "MKQLEDKVEELLSKNYHLENEVARLKKLV", "abcdefgabcdefgabcdefgabcdefga") ## ----DisplayResultForGCN4WildType---------------------------------------- GCN4wt ## ----PlotResultForGCN4WildType,fig.width=7,fig.height=5,out.width='0.6\\textwidth'---- plot(GCN4wt) ## ----PredictMarcoilExample----------------------------------------------- res <- predict(PrOCoilModel, "MGECDQLLVFMITSRVLVLSTLIIMDSRQVYLENLRQFAENLRQNIENVHSFLENLRADLENLRQKFPGKWYSAMPGRHG", "-------------------------------abcdefgabcdefgabcdefgabcdefgabcdefg--------------") ## ----DisplayResultForMarcoilExample-------------------------------------- res ## ----PlotResultForMarcoilExample,fig.width=8,fig.height=5,out.width='0.7\\textwidth'---- plot(res[1]) ## ----PredictGCN4Mutation------------------------------------------------- GCN4mSeq <- c("GCN4wt" ="MKQLEDKVEELLSKNYHLENEVARLKKLV", "GCN4_N16Y_L19T"="MKQLEDKVEELLSKYYHTENEVARLKKLV", "GCN4_E22R_K27E"="MKQLEDKVEELLSKNYHLENRVARLEKLV", "GCN4_V23K_K27E"="MKQLEDKVEELLSKNYHLENEKARLEKLV") GCN4mReg <- rep("abcdefgabcdefgabcdefgabcdefga", 4) GCN4mut <- predict(PrOCoilModel, GCN4mSeq, GCN4mReg) GCN4mut ## ----PlotGCN4Mutation,fig.width=7,fig.height=5,out.width='0.6\\textwidth'---- plot(GCN4mut[c(1, 2)]) plot(GCN4mut[c(1, 3)]) plot(GCN4mut[c(1, 4)]) ## ----HeatmapGCN4Mutation,fig.width=8,fig.height=4.5,out.width='0.9\\textwidth'---- heatmap(GCN4mut) ## ----PlotResultForExampleWithHeptadIrregularity,fig.width=7,fig.height=5,out.width='0.6\\textwidth'---- plot(predict(PrOCoilModel, "LQDTLVRQERPIRKSIEDLRNTV", "defgabcdefgabcdabcdefga")) ## ----ReadModelFile,eval=FALSE-------------------------------------------- ## URL <- "http://www.bioinf.jku.at/software/procoil/PrOCoilModel_v2.CCModel" ## myModel <- readCCModel(URL) ## ----CustomPlot,fig.width=7,fig.height=5,out.width='0.6\\textwidth'------ plot(GCN4mut[c(1, 2)], legend=c("wild type", "mutant N16Y,L19T"), col=c(rgb(0.7, 0, 0), rgb(0, 0, 0.8)), main="GCN4 Mutation Analysis", shades=c(rgb(0.77, 0.85, 0.95), rgb(0.99, 0.84, 0.71))) ## ----PlotProfileToGraphicsFile,eval=FALSE-------------------------------- ## pdf(file="GCN4wt.pdf", height=6, ## width=max(nchar(sequences(GCN4wt))) * 6 / 24) ## plot(GCN4wt) ## dev.off() ## ## bmp(file="GCN4wt.bmp", height=480, ## width=max(nchar(sequences(GCN4wt))) * 480 / 24) ## plot(GCN4wt) ## dev.off() ## ----GCN4CharacterExampleWithAttribute----------------------------------- GCN4wtSeq1 <- "MKQLEDKVEELLSKNYHLENEVARLKKLV" attr(GCN4wtSeq1, "reg") <- "abcdefgabcdefgabcdefgabcdefga" res <- predict(PrOCoilModel, GCN4wtSeq1) ## ----GCN4AAStringExampleWithMetadata------------------------------------- GCN4wtSeq2 <- AAString("MKQLEDKVEELLSKNYHLENEVARLKKLV") metadata(GCN4wtSeq2)$reg <- "abcdefgabcdefgabcdefgabcdefga" res <- predict(PrOCoilModel, GCN4wtSeq2) ## ----GCN4AAStringSetExampleWithAnnotationMetadata------------------------ GCN4mSeq2 <- AAStringSet(GCN4mSeq) annotationMetadata(GCN4mSeq2, annCharset="abcdefg") <- GCN4mReg res <- predict(PrOCoilModel, GCN4mSeq2) ## ----DisplayModels------------------------------------------------------- PrOCoilModel weights(PrOCoilModel)["N..La..d"] PrOCoilModelBA weights(PrOCoilModelBA)["N..La..d"] ## ----DisplayWeights------------------------------------------------------ noP <- length(weights(PrOCoilModel)) names(weights(PrOCoilModel))[1:25] names(weights(PrOCoilModel))[noP:(noP - 24)] ## ----DisplayBibTeXReference,eval=FALSE----------------------------------- ## toBibtex(citation("procoil"))