digestMod: modified 'Digest' function (from OrgMassSpecR package)

Description Usage Arguments Details Value Examples

View source: R/digestMod.R

Description

allows maxCharge to be set to calculate precursor m/z

Usage

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digestMod(sequence, enzyme = "trypsin", missed = 0, 
maxCharge = 8,IAA = TRUE, N15 = FALSE, custom = list())

Arguments

sequence

a character string representing the amino acid sequence.

enzyme

is the enzyme to perform in silico digestion with

missed

the maximum number of missed cleavages. Must be an integer of 0 (default) or greater. An error will result if the specified number of missed cleavages is greater than the maximum possible number of missed cleavages.

maxCharge

numeric max charge charge for predicted precursor m/z

IAA

logical. TRUE specifies iodoacetylated cysteine and FALSE specifies unmodified cysteine. Used only in determining the elemental formula, not the three letter codes.

N15

logical indicating if the nitrogen-15 isotope should be used in place of the default nitrogen-14 isotope. calculation

custom

list of custom masses

Details

see Digest for details of further function arguments.

Value

dataframe

Examples

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digestMod('MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIA',
enzyme = "trypsin", missed = 0, maxCharge = 8,IAA = TRUE, N15 = FALSE, 
custom = list()) 

adductomicsR documentation built on Nov. 8, 2020, 4:49 p.m.