## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 6, fig.height = 4 ) ## ----------------------------------------------------------------------------- library(idpr) #Attach the package p53_ID <- "P04637" iupred(p53_ID, proteinName = "HUMAN P53") ## ----------------------------------------------------------------------------- #BiocManager::install("idpr") ## ----------------------------------------------------------------------------- #devtools::install_github("wmm27/idpr") ## ----------------------------------------------------------------------------- library(idpr) #Attach the package ## ----------------------------------------------------------------------------- p53_ID <- "P04637" iupred(p53_ID, proteinName = "HUMAN P53", iupredType = "long") ## ----------------------------------------------------------------------------- iupredLongDF <- iupred(p53_ID, proteinName = "HUMAN P53", iupredType = "long", plotResults = FALSE) head(iupredLongDF) ## ----------------------------------------------------------------------------- p53_ID <- "P04637" iupred(p53_ID, proteinName = "HUMAN P53", iupredType = "short") ## ----------------------------------------------------------------------------- iupredShortDF <- iupred(p53_ID, iupredType = "short", plotResults = FALSE) head(iupredShortDF) ## ----------------------------------------------------------------------------- p53_ID <- "P04637" iupred(p53_ID, proteinName = "HUMAN P53", iupredType = "glob") ## ----------------------------------------------------------------------------- iupredGlobDF <- iupred(p53_ID, iupredType = "glob", plotResults = FALSE) head(iupredGlobDF) ## ----------------------------------------------------------------------------- p53_ID <- "P04637" iupredAnchor(p53_ID, proteinName = "HUMAN P53") ## ----------------------------------------------------------------------------- iupredAnchorDF <- iupredAnchor(p53_ID, plotResults = FALSE) head(iupredAnchorDF) ## ----------------------------------------------------------------------------- p53_ID <- "P04637" iupredRedox(p53_ID, proteinName = "HUMAN P53") ## ----------------------------------------------------------------------------- iupredRedoxDF <- iupredRedox(p53_ID, plotResults = FALSE) head(iupredRedoxDF) ## ----------------------------------------------------------------------------- iupredLongDF <- iupred(p53_ID, proteinName = "HUMAN P53", iupredType = "long", plotResults = FALSE) sequenceMap(sequence = iupredLongDF$AA, property = iupredLongDF$IUPred2, customColors = c("darkolivegreen3", "grey65", "darkorchid1")) + ggplot2::labs(title = "Prediction of Intrinsic Disorder in HUMAN P53", subtitle = "By IUPred2A long") ## ----------------------------------------------------------------------------- citation("ggplot2") ## ----------------------------------------------------------------------------- R.version.string ## ----------------------------------------------------------------------------- as.data.frame(Sys.info()) ## ---- results="asis"---------------------------------------------------------- citation()