inst/doc/iupred-vignette.R

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6, 
  fig.height = 4
)

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library(idpr) #Attach the package

p53_ID <- "P04637"
iupred(p53_ID,
       proteinName = "HUMAN P53")

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#BiocManager::install("idpr") 

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#devtools::install_github("wmm27/idpr")

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library(idpr) #Attach the package

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p53_ID <- "P04637"
iupred(p53_ID,
       proteinName = "HUMAN P53",
       iupredType = "long")

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iupredLongDF <- iupred(p53_ID,
                       proteinName = "HUMAN P53",
                       iupredType = "long",
                       plotResults = FALSE)
head(iupredLongDF)

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p53_ID <- "P04637"
iupred(p53_ID,
       proteinName = "HUMAN P53",
       iupredType = "short")

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iupredShortDF <- iupred(p53_ID,
                        iupredType = "short",
                        plotResults = FALSE)
head(iupredShortDF)

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p53_ID <- "P04637"
iupred(p53_ID,
       proteinName = "HUMAN P53",
       iupredType = "glob")

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iupredGlobDF <- iupred(p53_ID,
                       iupredType = "glob",
                       plotResults = FALSE)
head(iupredGlobDF)

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p53_ID <- "P04637"
iupredAnchor(p53_ID,
             proteinName = "HUMAN P53")

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iupredAnchorDF <- iupredAnchor(p53_ID, 
                               plotResults = FALSE)
head(iupredAnchorDF)

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p53_ID <- "P04637"
iupredRedox(p53_ID,
             proteinName = "HUMAN P53")

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iupredRedoxDF <- iupredRedox(p53_ID, 
                             plotResults = FALSE)
head(iupredRedoxDF)

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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")


                         

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citation("ggplot2")

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R.version.string

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as.data.frame(Sys.info())

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citation()