scoreProteinFragments: Scoring Of Identifications (For Multi-Protein Queries)

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

Scoring Of Identifications (For Multi-Protein Queries)

Description

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

Usage

scoreProteinFragments(
  resTab,
  fragmInp = NULL,
  j = 2,
  useCol = c("orig", "precAA", "tailAA", "beg", "end", "ppmToPred", "obsInd", "predInd"),
  prefFragPat = NULL,
  contigTermFragWe = 0.5,
  returnCombined = TRUE,
  figDraw = TRUE,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

resTab	(matrix or data.frame) identification results (will use columns 'beg','end','orig','obsInd')
fragmInp	(numeric vector or matrix) experimental m/z values, may include suppl col(s) to be considered for score (se argument 'j')
j	(integer) which column of fragmInp has m/z values, the following column is assumed as peak-intensity
useCol	(character) colnames from resTab to be used, 1st posiion must be present as column of 'resTab' and must represent name of original, used for splitting by proteins (eg original input protein sequence), will be passed to scoreFragments
prefFragPat	(matrix) for preferential fragmentation rules (see .prefFragPattern())
contigTermFragWe	(numeric, length=1) weight to add for terminal fragments (since they cannot match other fragments beyond the protein limits)
returnCombined	(logical)
figDraw	(logical) make additional figure
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of message(s) produced
debug	(logical) for bug-tracking: more/enhanced messages and intermediate objects written in global name-space

Value

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

See Also

scoreFragments, identifyPepFragments

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)))
(out <- scoreProteinFragments(tab2, fragmInp=cbind(as.numeric(obsMassX), Abundance=1)))

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