wrTopDownFrag (version 1.0.4)

modifFragmTabOutput: 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
)

Value

data.frame of reorganized identification results

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

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))