wrTopDownFrag (version 1.0.4)

.exNamesTyDeList: 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
)

Value

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

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

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)