scaledHydropathyLocal: Calculate the Average Scaled Hydropathy of an Amino Acid...

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

Calculate the Average Scaled Hydropathy of an Amino Acid Sequence

Description

This is used to calculate the scaled hydropathy of an amino acid sequence using a sliding window. The output is either a data frame or graph showing the calculated scores for each window along the sequence.

Usage

scaledHydropathyLocal(
  sequence,
  window = 9,
  plotResults = TRUE,
  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.
window	a positive, odd integer. 9 by default. Sets the size of sliding window, must be an odd number. The window determines the number of residues to be analyzed and averaged for each position along the sequence.
plotResults	logical value, TRUE by default. If plotResults = TRUE a plot will be the output. If plotResults = FALSE the output is a data frame with scores for each window analyzed.
proteinName	character string with length = 1. optional setting to replace the name of the plot if hydropathy = TRUE.
...	any additional parameters, especially those for plotting.

Value

see plotResults argument

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(), scaledHydropathyGlobal()

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

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

#Changing window will alter the number of residues analyzed
exampleDF_window3 <- scaledHydropathyLocal(aaString,
                                           window = 3,
                                           plotResults = FALSE)
head(exampleDF_window3)
exampleDF_window15 <- scaledHydropathyLocal(aaString,
                                            window = 15,
                                            plotResults = FALSE)
head(exampleDF_window15)

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

#since it is a ggplot, you can change or annotate the plot
 gg <- scaledHydropathyLocal(aaVector,
                             window = 3,
                             plot = TRUE)
 gg <- gg + ggplot2::ylab("Local Hydropathy")
  gg <- gg + ggplot2::geom_text(data = exampleDF_window3,
                               ggplot2::aes(label = CenterResidue,
                                            y = WindowHydropathy + 0.1))
 plot(gg)

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