scoreChargeCatch {wrTopDownFrag}

Scoring of charge catching potential for peptides

Description

Make score based on cumulative search for AA with given potential to catch charge (H+, or optionally any charge). Note : at current cumulative scoring large peptides may get priviliged.

Usage

scoreChargeCatch(
  resTab,
  pepCol = "seq",
  scale01 = TRUE,
  chargeMode = "pos",
  silent = FALSE,
  callFrom = NULL
)

Arguments

resTab

(matrix or data.frame) matrix or data.frame of results for SINGLE protein (here only the column specified with argument 'pepCol' will be used)

pepCol

(character) column name of 'resTab' containing the peptide sequence to be scored

scale01

(logical) linear rescale output to maximum 1.0

chargeMode

(character) this value may be 'pos' (default) for the positively charged amino-acids K,R and H or, if this argument has any other value, than all charged amino-acids (K,R,H, S,T,N,Q, D,E, W and Y) will be considered.

silent

(logical) suppress messages

callFrom

(character) allow easier tracking of message(s) produced

Value

numeric vector with score for each peptide of resTab (even if scale01=TRUE minimum may be >0 if all peptides do contain charge-catching AAs)

See Also

fragmentSeq

Examples

resTa <- matrix(c(1:4,"PEPTID","PEPTIK","PEPTRK","AGV"), ncol=2,
  dimnames=list(NULL,c("predInd","seq"))) 
scoreChargeCatch(resTa)