chemScore: ChemScore

Description Usage Arguments References Examples

View source: R/chemScore.R

Description

This function calculates the ChemScore proposed in Parker 2001.

Usage

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chemScore(x, arg = 100, cys = 0, lys = 10, detrimentalCys = 10,
  metOxF = 0.2, nMetOx = 1L, verbose = interactive())

Arguments

x

character, amino acid sequence(s).

arg

double, base ChemScore for Arginine (default: 100).

cys

double, base ChemScore for Cysteine (default: 0).

lys

double, base ChemScore for Lysine (default: 10).

detrimentalCys

double, score for detrimental cysteine.

metOxF

double, methionine oxidation factor (default: 0.2).

nMetOx

integer, number of oxidized methionine (default: 1).

verbose

logical, verbose output?

References

Parker KC. Scoring methods in MALDI peptide mass fingerprinting: ChemScore, and the ChemApplex program.
Journal of the American Society for Mass Spectrometry. 2002 Jan 31;13(1):22-39.

Examples

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library("detectability")

# Example sequences taken from Table 4 in Parker 2001.
sequences <- c("HGLDNYR",
               "RHGLDNYR",
               "WWCNDGR",
               "GTDVQAWIR",
               "GYSLGNWVCAAK",
               "FESNFNTQATNR",
               "IVSDGNGMNAWVAWR",
               "NTDGSTDYGILQINSR",
               "KIVSDGNGMNAWVAWR")
chemScore(sequences)

sgibb/detectability documentation built on May 26, 2017, 6:55 a.m.