dot-exNamesTyDeList: Reorganize List Of Peptide Fragments To Matrix

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

Reorganize List Of Peptide Fragments To Matrix

Description

This function allows reorganiziong a list (of lists) of peotide fragments into matrix

Usage

.exNamesTyDeList(
  x,
  subLiNames = c("full", "Nter", "Cter", "inter"),
  inclNo = TRUE,
  fullSeq = NULL,
  outCol = c("seq", "orig", "origNa", "ty", "seqNa", "beg", "end", "precAA", "tailAA",
    "ambig", "mass"),
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

x	(list) list of lists with charcter vectors of sequences with names that can be parsed eg 'x.1-7' to extract 'beg'&'end' otherwise ALL output will be NA (+message form extractLast2numericParts())
subLiNames	(character)
inclNo	(logical) add 1st col with number
fullSeq	(character) to reinject full sequence which may not be used in names of 'x' and not be in x[[1]][["full"]]
outCol	(character) columns to create in output
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of message(s) produced
debug	(logical) for bug-tracking: more/enhanced messages

Value

This function returns matrix with fragment sequence, mass, start- and end-position, heading and tailing AA (or NA if terminal fragment)

See Also

makeFragments; evalIsoFragm, from package wrProteo convAASeq2mass, AAmass, massDeFormula

Examples

prot1 <- c(protP="KEPTIDE", pro2="MPRATE")
## fragment all target proteins
pep3 <- lapply(prot1, fragmentSeq, minSize=3, maxSize=5, internFragments=FALSE, 
  separTerm=TRUE, keepRedSeqs=TRUE)
pepTab <- .exNamesTyDeList(pep3, fullSeq=prot1) 

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