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

In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

Description

allows maxCharge to be set to calculate precursor m/z

Usage

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

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

JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.