modifFragmTabOutput: Change fragment identification output format (for biologists)

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

Change fragment identification output format (for biologists)

Description

Change fragment identification output to format better adopted for biologists

Usage

modifFragmTabOutput(
  datafr,
  addData = NULL,
  fuseC = c("precAA", "seq", "tailAA"),
  sep = ".",
  modifCol = "mod",
  replMod = cbind(old = "by", new = "i"),
  finCols = c("fraNa", "origNa", "beg", "end", "seq", "ty", "mod", "modSpec", "obsMass",
    "mass", "ppmToPred", "ambig", "runNo", "FDR", "sco4", "sc.prefFrag",
    "sc.chargeCatch", "sc.complemFra", "sc.sameSite", "logInt"),
  supFinCols = NULL,
  sortTable = "end",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

datafr	(data.frame) initial output from identifyPepFragments()
addData	(matrix or data.frame) suppelemental data
fuseC	(character) columns to exract preceeding and tailing AA to fuse with separator 'sep' to main sequence
sep	(character) separator for concatenation
modifCol	(character) default 'modif'
replMod	(matrix) if names of modifications shoule be renamed : the columns 'old' and 'new' indicata how modifcations should be renamed
finCols	(character) columns to retain for final output
supFinCols	(character)
sortTable	(character) sort output 1st by name, then by 'beg' or 'end'
silent	(logical) suppress messages
debug	(logical) addtional diagnostic messages
callFrom	(character) allow easier tracking of message produced

Value

data.frame of reorganized identification results

See Also

identifyPepFragments

Examples

protP <- c(protP="PEPTIDE")
obsMassX <- cbind(a=c(199.1077,296.1605,397.2082,510.2922,625.3192),
  b=c(227.1026,324.1554,425.2031,538.2871,653.3141),
  x=c(729.2937,600.2511,503.1984,402.1507,289.0666),
  y=c(703.3145,574.2719,477.2191,376.1714,263.0874))
rownames(obsMassX) <- c("E","P","T","I","D")      # all 1 & 7 ions not included
modTy1 <- list(basMod=c("b","y"), varMod=c("p","o","q"))
frag1 <- identifyPepFragments(ex=as.numeric(obsMassX), pe=protP, modTy=modTy1, 
  minFragSize=2, chargeCatchFilter=FALSE)
(frag1b <- if(length(unlist(frag1$identif)) >0) modifFragmTabOutput(frag1))

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