scaledHydropathyGlobal: Protein Scaled Hydropathy Calculations

In wmm27/idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Protein Scaled Hydropathy Calculations

Description

This is used to calculate the scaled hydropathy of an amino acid sequence for each residue in the sequence. The output is either a data frame or graph showing the matched scores for each residue along the sequence.

Usage

scaledHydropathyGlobal(sequence, plotResults = FALSE, proteinName = NA, ...)

Arguments

sequence	amino acid sequence as a single character string, a vector of single characters, or an AAString object. It also supports a single character string that specifies the path to a .fasta or .fa file.
plotResults	logical value, FALSE by default. If plotResults = TRUE a plot will be the output. If plotResults = FALSE the output is a data frame for each residue.
proteinName	character string with length = 1. optional setting to include the name in the plot title.
...	any additional parameters, especially those for plotting.

Value

if plotResults = TRUE, a graphical representation data. Average is shown by the horizontal line. If plotResults = FALSE, a data frame is reported with each amino acid and each residue value shown. Score for each residue shown in the column "Hydropathy".

Plot Colors

For users who wish to keep a common aesthetic, the following colors are used when plotResults = TRUE.

• Dynamic line colors:

  • Close to 0 = "skyblue3" or "#6CA6CD"

  • Close to 1 = "chocolate1" or "#FF7F24"

  • Close to midpoint = "grey65" or "#A6A6A6"

References

Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of molecular biology, 157(1), 105-132.

See Also

KDNorm for residue values.

Other scaled hydropathy functions: KDNorm, foldIndexR(), meanScaledHydropathy(), scaledHydropathyLocal()

Examples

#Amino acid sequences can be character strings
aaString <- "ACDEFGHIKLMNPQRSTVWY"
#Amino acid sequences can also be character vectors
aaVector <- c("A", "C", "D", "E", "F",
              "G", "H", "I", "K", "L",
              "M", "N", "P", "Q", "R",
              "S", "T", "V", "W", "Y")
#Alternatively, .fasta files can also be used by providing
##The path to the file as a character string

exampleDF <- scaledHydropathyGlobal(aaString,
                                    plotResults = FALSE)
head(exampleDF)

exampleDF <- scaledHydropathyGlobal(aaVector,
                                    plotResults = FALSE)
head(exampleDF)

#plotResults = TRUE will output a ggplot
  scaledHydropathyGlobal(aaString,
                         plotResults = TRUE)

  #since it is a ggplot, you can change or annotate the plot
  gg <- scaledHydropathyGlobal(aaVector,
                               plotResults = TRUE)
  gg <- gg + ggplot2::ylab("Local Hydropathy")
  gg <- gg + ggplot2::geom_text(data = exampleDF,
                                ggplot2::aes(label = AA,
                                             y = Hydropathy + 0.1))
  plot(gg)

wmm27/idpr documentation built on Jan. 12, 2023, 8:45 a.m.