netCharge {idpr} | R Documentation

## Protein Charge Calculation, Net Charge

### Description

This function will determine the net charge of a peptide using the Henderson-Hasselbalch Equation. The output is a numeric value describing the total net charge or the average net charge.

### Usage

    netCharge(
      sequence,
      pKaSet = "IPC_protein",
      pH = 7,
      includeTermini = TRUE,
      averaged = FALSE
    )

### Arguments

`sequence` | amino acid sequence as a character string or vector of individual residues. alternatively, a character string of the path to a .fasta / .fa file
`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.
`pH` | numeric value, 7.0 by default. The environmental pH used to calculate residue charge.
`includeTermini` | Logical value, TRUE by default. This determines how the calculation handles the N- and C- terminus. includeTermini determines if the calculation will use the charge of the amine and carboxyl groups at the ends of the peptide (When TRUE). These charges are ignored when `includeTermini = FALSE`.
`averaged` | logical value. FALSE by default. When `averaged = FALSE`, the total net charge is returned. When `averaged = TRUE`, the total net charge is averaged by the sequence length. This gives a value of -1 to +1.

### Value

numeric value. Either the net charge or average net charge, depending on the value of the averaged argument

### See Also

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

Other charge functions: `chargeCalculationGlobal()`, `chargeCalculationLocal()`, `hendersonHasselbalch()`

### 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.

    #Calculate the Net Charge
    netCharge(aaString,
              averaged = FALSE)
    netCharge(aaVector,
              averaged = FALSE)

    #Calculate the Average Net Charge
    netCharge(aaString,
              averaged = TRUE)
    netCharge(aaVector,
              averaged = TRUE)

    #Change the pH
    netCharge(aaString,
              pH = 8)
    netCharge(aaString,
              pH = 7)
    netCharge(aaString,
              pH = 5.5)

    #Specify which pKa set to use
    netCharge(aaString,
              pKaSet = "IPC_protein") #Default
    netCharge(aaString,
              pKaSet = "IPC_peptide")
    netCharge(aaString,
              pKaSet = "Dawson")
    netCharge(aaString,
              pKaSet = "EMBOSS")

    #Should the termini be included in charge calculations?
    netCharge(aaString,
              includeTermini = TRUE) #Default
    netCharge(aaString,
              includeTermini = FALSE)

[Package idpr version 1.2.0 Index]