wrTopDownFrag (version 1.0.4)

scoreFragments: Scoring For Single Protein : Individual Components

Description

Make scoring for single protein : individual components :sameSite,contiguous,prefFragSite,logPeakHeight + combined (sum of scales 0->1)

Usage

scoreFragments(
  resTab,
  fragmInp,
  suplTakeLog = TRUE,
  j = NULL,
  useResCol = c("orig", "seq", "precAA", "tailAA", "beg", "end", "ppmToPred", "obsInd",
    "predInd", "Abundance"),
  prefFragPat = NULL,
  contigTermFragWe = 0.5,
  figDraw = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a list with matrix $scaled (combined and indiv rescaled scores) and $raw (matching lines of 'resTab'; 'index' refers to predictedIndex)

Arguments

resTab

(matrix or data.frame) matrix or data.frame of results for SINGLE protein (will use columns 'beg','end','orig','obsInd')

fragmInp

(matrix) experimental m/z values including suppl col(s) to be considered for score, its intensity column/value will be used for 'logInt' in output

suplTakeLog

(logical) if suppl info should be used as log2: if T all supplemental data columns ('fragmInp') will be taken as log2

j

(integer) which column of fragmInp has m/z values, the following column is assumed as peak-intensity

useResCol

(character) column-names from resTab to be used

prefFragPat

(matrix) for preferential fragmentation rules (see .prefFragPattern())

contigTermFragWe

(numeric, length=1) weight to add for terminal fragments at 'sc.complemFra' (since they cannot match other fragments beyond the protein limits)

figDraw

(logical) make additional figure

silent

(logical) suppress messages

debug

(logical) additional messages and objects exportet to current session for debugging

callFrom

(character) allow easier tracking of messages produced

See Also

identifyPepFragments, scoreProteinFragments

Examples

tab2 <- matrix(c("20","2","13","11","3","10","4", "PT","PE","EP","DE","PEP","IDE","PEPT", 
  rep(c("PEPTIDE","protP"),each=7), c("inter","Nter","Cter")[c(1,2,1,3,2,3,2)], 
  c(3,1,2,6,1,5,1, 4,2,3,7,3,7,4), "E",NA,"P","I",NA,"T",NA, "I","P","T",NA,"T",NA,"I", 
  c(1,6,6,20,7,19,8), c(-0.094312,-0.14707,-0.14707,0.08641,0.0084762,-0.10965,0.057087), 
  rep(2,7)), nrow=7, dimnames=list(NULL,c("predInd","seq","orig","origNa","ty","beg","end",
  "precAA","tailAA","obsInd","ppmToPred","mass")))
tab2 <- cbind(tab2, seqNa=paste0(tab2[,"origNa"],".",tab2[,"beg"],"-",tab2[,"end"]),Abundance=1)
rownames(tab2) <- paste0(tab2[,"origNa"],".", tab2[,"beg"],"", tab2[,"end"])
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))

(outF <- scoreFragments(tab2, fragmInp=cbind(as.numeric(obsMassX), Abundance=1)))