charge
calculates the net charge of amino acid sequences using
the method of Moore, 1985, with exclusion of the C-terminus and N-terminus charges.
charge(seq, pH = 7.4, pK = NULL, normalize = FALSE)
A vector of net charges for the sequence(s).
vector strings defining of amino acid sequences.
environmental pH.
named vector defining pK values for each charged amino acid,
where names are the single-letter amino acid character codes
c("R", "H", "K", "D", "E", "C", "Y")
). If NULL
,
then the EMBOSS scale is used.
if TRUE
then divide the net charge of each amino acid
sequence by the number of informative positions. Non-informative
position are defined by the presence any character in
c("X", "-", ".", "*")
. If FALSE
then return the raw
net charge.
Moore DS. Amino acid and peptide net charges: A simple calculational procedure. Biochem Educ. 13, 10-11 (1985).
https://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html
For additional pK scales see pK
.
seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT")
# Unnormalized charge
charge(seq)
# Normalized charge
charge(seq, normalize=TRUE)
# Use the Murray et al, 2006 scores from the seqinr package
library(seqinr)
data(pK)
x <- setNames(pK[["Murray"]], rownames(pK))
# Calculate charge
charge(seq, pK=x)
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