wrTopDownFrag (version 1.0.4)

.termPepCut: Make Named Character Vector Of Sequential Terminal Fragments

Description

Make named character vector of sequential terminal fragments

Usage

.termPepCut(
  pe,
  mi,
  ma = 1000,
  se1 = ".",
  se2 = "-",
  mainName = NULL,
  sepNC = FALSE,
  indexOffs = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a numeric vector with mass(es) and sequence in name(s)

Arguments

pe

(character, length=1) s

mi

(integer) min number of AA residues for considering peptide fragments; should be <= length(pe) (otherwise the full length of 'pe' ALWAYS returned !)

ma

(integer) max number of AA residues for considering peptide fragments

se1

(character, length=1) separators for adding numbers to specify partial/fragment locations

se2

(character, length=1) separators for adding numbers to specify partial/fragment locations

mainName

(character, length=1)

sepNC

(logical) if 'TRUE', separate N-terminal, C-terminal and internal fragments in list

indexOffs

(logical) offset to add for custom numbering in names (numeric, length=1), ie '1' will already increase by +1

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

See Also

makeFragments; convAASeq2mass

Examples

## Ubiquitin example
P0CG48 <- "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"  
.termPepCut(P0CG48, mi=3, ma=12 ,sepNC=TRUE, mainName="P0CG48")