combinateAllAndSum {wrTopDownFrag}

Full combinatorial and cumulative values

Description

Use for all preparing all combinations of non-compulsatory, ie variable, mass modifications Variable modifications may or may not be present. Thus, for a given amino-acid with a variable modification two versions of the molecular weight need to be considered. Most (variable) modifications are linked to a type of amino acid, like serine-residues for phosphorlylation. Thus in this case, each instance of the amino acid in question may or may not be modified. So, for example if there are 2 serines, 0, 1 or 2 phosphorylation modifications may be present. For this reason the is the argument nMax to stay within biologically relevant ranges (external knowledge) and reduce complexity significantly. Some modifications are exclusive to others, argument notSingle : An (artificially occuring) de-phosphorylation event during fragmentation can only happen if the amino acid was already phosphorylated in the first place.

Usage

combinateAllAndSum(
  nMax,
  modVal,
  notSingle = NULL,
  silent = TRUE,
  callFrom = NULL
)

Arguments

nMax

(integer or data.frame with 1 line) maximum number of modifications

modVal

(numeric, has to have names !) the change of molecular mass introduced by given modifications (as specified by the name of the value)

notSingle

(character) names of 'modVal' where 1st element of 'notSingle' cannot happen/appear if 2nd element not present (eg de-phospho/phosphorylation)

silent

(logical) suppress messages

callFrom

(character) allow easier tracking of message(s) produced

Value

named (concatenated names of modVal) numeric vector

See Also

convToNum

Examples

## to follow easily the results, hypothetical mass-modification values were chosen
mo1 <- c(a=10, b=1, c=0.1, d=0.01); nMa1 <- c(1,2,0,3)
combinateAllAndSum(nMa1, mo1)
## # like 'b' for phospho & 'd' for de-phospho (which can't happen without phospho event)
combinateAllAndSum(nMa1, mo1, notSingle=c("d","b"))