chargeCalculationLocal: Charge Calculation Along a Protein Sequence

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

Charge Calculation Along a Protein Sequence

Description

This calculates the charge, as determined by the Henderson-Hasselbalch equation, for each window along the sequence. This function uses a sliding window. The output is either a graph or a data frame of calculated charges.

Usage

chargeCalculationLocal(
  sequence,
  window = 9,
  proteinName = NA,
  pH = 7,
  pKaSet = "IPC_protein",
  printCitation = FALSE,
  plotResults = FALSE,
  ...
)

Arguments

sequence	amino acid sequence as a single character string or vector of single characters. It also supports a single character string that specifies the location of 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.
proteinName	character string, optional. Used to add protein name to the title in ggplot. Ignored if plotResults = FALSE.
pH	numeric value, 7.0 by default. The environmental pH used to calculate residue charge.
pKaSet	A character string or data frame. "IPC_protein" by default. Character string to load specific, preloaded pKa sets. c("EMBOSS", "DTASelect", "Solomons", "Sillero", "Rodwell", "Lehninger", "Toseland", "Thurlkill", "Nozaki", "Dawson", "Bjellqvist", "ProMoST", "Vollhardt", "IPC_protein", "IPC_peptide") Alternatively, the user may supply a custom pKa dataset. The format must be a data frame where: Column 1 must be a character vector of residues named "AA" AND Column 2 must be a numeric vector of pKa values.
printCitation	Logical value. FALSE by default. When printCitation = TRUE the citation for the pKa set is printed. This allows for the user to easily obtain the dataset citation. Will not print if there is a custom dataset.
plotResults	logical value. TRUE by default. If plotResults = TRUE, a ggplot of window charges are returned. If plotResults = FALSE, a data frame of window charges are returned.
...	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 -1 = "#92140C"

  • Close to +1 = "#348AA7"

  • Close to 0 (midpoint) = "grey65" or "#A6A6A6"

See Also

pKaData for residue pKa values and citations. See hendersonHasselbalch for charge calculations.

Other charge functions: chargeCalculationGlobal(), hendersonHasselbalch(), netCharge()

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
# a character string of the path to the file.
exampleDF <- chargeCalculationLocal(aaString)
exampleDF <- chargeCalculationLocal(aaVector)
head(exampleDF)

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

#Changing pKa set or pH used for calculations
exampleDF_pH5 <- chargeCalculationLocal(aaString,
                                        pH = 5)
head(exampleDF_pH5)
exampleDF_pH7 <- chargeCalculationLocal(aaString,
                                       pH = 7)
head(exampleDF_pH7)
exampleDF_EMBOSS <- chargeCalculationLocal(aaString,
                                           pH = 7,
                                           pKa = "EMBOSS")
head(exampleDF_EMBOSS)

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

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

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