scaledHydropathyLocal {idpr} | R Documentation

## 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. 7 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`, `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)

[Package idpr version 1.2.0 Index]