dot-termPepCut: Make Named Character Vector Of Sequential Terminal Fragments

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

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
)

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

Value

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

See Also

makeFragments; convAASeq2mass

Examples

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

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.